Starting phenix.real_space_refine on Thu Feb 15 08:39:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/02_2024/6g72_4356_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 8 5.49 5 S 488 5.16 5 C 41824 2.51 5 N 10938 2.21 5 O 11637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "D ARG 2": "NH1" <-> "NH2" Residue "D ARG 133": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 378": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 218": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 268": "NH1" <-> "NH2" Residue "G TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 285": "NH1" <-> "NH2" Residue "G ARG 359": "NH1" <-> "NH2" Residue "H PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 25": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L ARG 262": "NH1" <-> "NH2" Residue "L ARG 436": "NH1" <-> "NH2" Residue "L ARG 535": "NH1" <-> "NH2" Residue "O ARG 145": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 76": "NH1" <-> "NH2" Residue "P ARG 102": "NH1" <-> "NH2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 31": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "V ARG 44": "NH1" <-> "NH2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "W ARG 33": "NH1" <-> "NH2" Residue "W ARG 79": "NH1" <-> "NH2" Residue "W ARG 107": "NH1" <-> "NH2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X ARG 144": "NH1" <-> "NH2" Residue "X ARG 146": "NH1" <-> "NH2" Residue "X PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 80": "NH1" <-> "NH2" Residue "Y ARG 103": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z ARG 26": "NH1" <-> "NH2" Residue "Z ARG 27": "NH1" <-> "NH2" Residue "Z ARG 48": "NH1" <-> "NH2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "a ARG 40": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "e ARG 50": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 100": "NH1" <-> "NH2" Residue "e ARG 104": "NH1" <-> "NH2" Residue "g ARG 57": "NH1" <-> "NH2" Residue "g ARG 89": "NH1" <-> "NH2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "i ARG 10": "NH1" <-> "NH2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 52": "NH1" <-> "NH2" Residue "l ARG 85": "NH1" <-> "NH2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 80": "NH1" <-> "NH2" Residue "n ARG 33": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 157": "NH1" <-> "NH2" Residue "n ARG 158": "NH1" <-> "NH2" Residue "o ARG 36": "NH1" <-> "NH2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 105": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ARG 15": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p ARG 65": "NH1" <-> "NH2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p ARG 92": "NH1" <-> "NH2" Residue "q ARG 60": "NH1" <-> "NH2" Residue "r ARG 5": "NH1" <-> "NH2" Residue "r ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 64924 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 10, 'TRANS': 144} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1712 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 15, 'TRANS': 190} Chain: "D" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3391 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 396} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, '2MR:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 21, 'TRANS': 190} Chain: "F" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3301 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 21, 'TRANS': 406} Chain: "G" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5296 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 31, 'TRANS': 656} Chain: "H" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2444 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 22, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1408 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 168} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1195 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'FME:plan-2': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'TYR:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 20, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2696 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 20, 'TRANS': 323} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2306 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 3 Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1015 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "R" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 748 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "S" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "U" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "W" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 970 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1152 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain: "a" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 548 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "b" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 389 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "d" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 985 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 12, 'TRANS': 106} Chain: "e" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 870 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "f" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 433 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1154 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 11, 'TRANS': 125} Chain: "i" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 820 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 89} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'SAC:plan-2': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "j" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 525 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Chain: "k" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 582 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "l" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1274 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 18, 'TRANS': 133} Chain: "m" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1035 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 11, 'TRANS': 112} Chain: "n" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1527 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 15, 'TRANS': 160} Chain: "o" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 898 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "p" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1438 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 10, 'TRANS': 159} Chain: "q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "r" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 796 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 336 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1502 SG CYS B 129 95.327 91.202 201.989 1.00 50.23 S ATOM 1005 SG CYS B 65 89.804 93.778 203.373 1.00 53.72 S ATOM 999 SG CYS B 64 89.315 87.969 200.761 1.00 52.24 S ATOM 1732 SG CYS B 159 92.040 88.655 206.345 1.00 48.96 S ATOM 7899 SG CYS E 103 111.406 45.034 258.385 1.00 82.79 S ATOM 7933 SG CYS E 108 110.420 41.911 259.732 1.00 83.52 S ATOM 8217 SG CYS E 144 114.884 42.506 254.828 1.00 80.89 S ATOM 8240 SG CYS E 148 113.758 39.642 256.118 1.00 85.00 S ATOM 11441 SG CYS F 362 117.824 49.446 234.419 1.00 60.14 S ATOM 11461 SG CYS F 365 114.484 50.003 239.122 1.00 59.62 S ATOM 11783 SG CYS F 405 117.903 44.939 238.692 1.00 63.35 S ATOM 11422 SG CYS F 359 120.666 51.291 239.328 1.00 63.02 S ATOM 12871 SG CYS G 114 114.029 67.989 224.027 1.00 52.32 S ATOM 12810 SG CYS G 105 108.517 71.080 226.000 1.00 49.53 S ATOM 12831 SG CYS G 108 114.312 73.034 227.374 1.00 51.88 S ATOM 13203 SG CYS G 156 122.377 61.856 229.589 1.00 52.52 S ATOM 13180 SG CYS G 153 120.123 64.710 234.977 1.00 53.95 S ATOM 13227 SG CYS G 159 126.055 64.986 232.778 1.00 57.00 S ATOM 13556 SG CYS G 203 121.249 67.856 229.378 1.00 55.01 S ATOM 12317 SG CYS G 41 122.091 54.600 226.224 1.00 54.95 S ATOM 12403 SG CYS G 52 118.012 55.016 226.335 1.00 56.19 S ATOM 12428 SG CYS G 55 119.482 50.911 222.747 1.00 55.38 S ATOM 12529 SG CYS G 69 122.227 52.691 222.876 1.00 57.67 S ATOM 20734 SG CYS I 121 95.977 83.521 212.770 1.00 47.63 S ATOM 20708 SG CYS I 118 97.217 90.292 213.874 1.00 48.92 S ATOM 20755 SG CYS I 124 97.934 86.005 217.917 1.00 45.77 S ATOM 20482 SG CYS I 89 101.680 86.391 212.566 1.00 47.83 S ATOM 20784 SG CYS I 128 100.583 83.051 225.337 1.00 46.68 S ATOM 20454 SG CYS I 85 104.535 84.863 220.417 1.00 45.72 S ATOM 20412 SG CYS I 79 105.528 87.455 225.552 1.00 49.12 S ATOM 20431 SG CYS I 82 106.319 81.091 225.259 1.00 48.06 S ATOM 40662 SG CYS R 59 102.863 79.245 241.013 1.00 56.17 S ATOM 40838 SG CYS R 84 106.265 80.557 239.592 1.00 54.23 S ATOM 40860 SG CYS R 87 103.224 82.250 238.190 1.00 53.49 S Time building chain proxies: 25.03, per 1000 atoms: 0.39 Number of scatterers: 64924 At special positions: 0 Unit cell: (184.87, 187.53, 289.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 488 16.00 P 8 15.00 O 11637 8.00 N 10938 7.00 C 41824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS X 65 " distance=2.03 Simple disulfide: pdb=" SG CYS X 45 " - pdb=" SG CYS X 55 " distance=2.03 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 17 " - pdb=" SG CYS Y 74 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 94 " - pdb=" SG CYS Y 114 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.04 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.04 Simple disulfide: pdb=" SG CYS o 68 " - pdb=" SG CYS o 79 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.04 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.30 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb=" SF4 B 201 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb=" SF4 F 502 " pdb="FE1 SF4 F 502 " - pdb=" SG CYS F 362 " pdb="FE2 SF4 F 502 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 502 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 502 " - pdb=" SG CYS F 405 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 124 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 89 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 121 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 118 " pdb="FE2 SF4 I 201 " - pdb=" NE2 HIS I 67 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 82 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 79 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 85 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 128 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 320 helices and 22 sheets defined 44.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.94 Creating SS restraints... Processing helix chain 'A' and resid 7 through 22 removed outlier: 4.212A pdb=" N ILE A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 19 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.969A pdb=" N PHE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.636A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 108 removed outlier: 3.747A pdb=" N ALA A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.854A pdb=" N LEU B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.576A pdb=" N GLU B 68 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 106 through 114 removed outlier: 4.005A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 175 removed outlier: 4.085A pdb=" N GLY B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 No H-bonds generated for 'chain 'B' and resid 183 through 186' Processing helix chain 'C' and resid 16 through 31 removed outlier: 3.501A pdb=" N GLN C 21 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 24 " --> pdb=" O GLN C 21 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C 25 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU C 31 " --> pdb=" O TYR C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 removed outlier: 3.598A pdb=" N VAL C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 4.217A pdb=" N THR C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 65 " --> pdb=" O THR C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 125 through 137 removed outlier: 4.353A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR C 130 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 133 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 134 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 12 No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.698A pdb=" N LEU D 106 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.713A pdb=" N ILE D 120 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 143 Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.633A pdb=" N ASN D 149 " --> pdb=" O THR D 145 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 through 159' Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.735A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 removed outlier: 4.103A pdb=" N PHE D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 229 removed outlier: 3.905A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 removed outlier: 3.814A pdb=" N ARG D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.550A pdb=" N LEU D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 5.052A pdb=" N SER D 263 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 277 through 280 Processing helix chain 'D' and resid 295 through 315 removed outlier: 3.674A pdb=" N MET D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 308 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 394 through 405 removed outlier: 3.519A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 402 " --> pdb=" O HIS D 398 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.762A pdb=" N VAL D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.521A pdb=" N GLU E 32 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 57 removed outlier: 3.984A pdb=" N ALA E 46 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL E 47 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 removed outlier: 3.644A pdb=" N ALA E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 84 removed outlier: 4.302A pdb=" N GLU E 82 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 113 through 123 removed outlier: 3.873A pdb=" N LYS E 123 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 176 removed outlier: 4.149A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 19 No H-bonds generated for 'chain 'F' and resid 17 through 19' Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 53 through 62 Processing helix chain 'F' and resid 77 through 82 removed outlier: 4.592A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 115 through 129 removed outlier: 3.543A pdb=" N GLY F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 3.922A pdb=" N LEU F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 191 through 196 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 231 through 235 Processing helix chain 'F' and resid 241 through 244 No H-bonds generated for 'chain 'F' and resid 241 through 244' Processing helix chain 'F' and resid 276 through 281 removed outlier: 3.992A pdb=" N ILE F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 343 through 355 removed outlier: 3.762A pdb=" N ILE F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 366 No H-bonds generated for 'chain 'F' and resid 363 through 366' Processing helix chain 'F' and resid 369 through 381 removed outlier: 3.986A pdb=" N LYS F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 398 removed outlier: 3.801A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU F 392 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP F 393 " --> pdb=" O ASP F 390 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE F 395 " --> pdb=" O LEU F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 removed outlier: 3.501A pdb=" N TRP F 413 " --> pdb=" O ASP F 409 " (cutoff:3.500A) Proline residue: F 414 - end of helix removed outlier: 3.645A pdb=" N HIS F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 435 removed outlier: 3.958A pdb=" N ARG F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 removed outlier: 4.039A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 91 No H-bonds generated for 'chain 'G' and resid 88 through 91' Processing helix chain 'G' and resid 94 through 99 removed outlier: 4.962A pdb=" N ALA G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.532A pdb=" N VAL G 199 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 266 through 268 No H-bonds generated for 'chain 'G' and resid 266 through 268' Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 296 through 307 removed outlier: 3.992A pdb=" N SER G 301 " --> pdb=" O GLU G 297 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 305 " --> pdb=" O SER G 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 338 removed outlier: 3.898A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 372 No H-bonds generated for 'chain 'G' and resid 370 through 372' Processing helix chain 'G' and resid 391 through 400 Processing helix chain 'G' and resid 426 through 434 removed outlier: 3.695A pdb=" N ILE G 432 " --> pdb=" O LEU G 429 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA G 433 " --> pdb=" O GLN G 430 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER G 434 " --> pdb=" O ASP G 431 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 444 Processing helix chain 'G' and resid 463 through 475 removed outlier: 4.043A pdb=" N LEU G 467 " --> pdb=" O GLY G 463 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G 469 " --> pdb=" O ALA G 465 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN G 472 " --> pdb=" O VAL G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 480 No H-bonds generated for 'chain 'G' and resid 477 through 480' Processing helix chain 'G' and resid 500 through 503 No H-bonds generated for 'chain 'G' and resid 500 through 503' Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 566 through 568 No H-bonds generated for 'chain 'G' and resid 566 through 568' Processing helix chain 'G' and resid 596 through 606 removed outlier: 4.047A pdb=" N ALA G 602 " --> pdb=" O LYS G 598 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 626 removed outlier: 3.771A pdb=" N GLU G 625 " --> pdb=" O ASN G 621 " (cutoff:3.500A) Processing helix chain 'G' and resid 643 through 650 Processing helix chain 'G' and resid 678 through 680 No H-bonds generated for 'chain 'G' and resid 678 through 680' Processing helix chain 'G' and resid 682 through 691 removed outlier: 4.126A pdb=" N CYS G 687 " --> pdb=" O THR G 683 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 8 removed outlier: 3.693A pdb=" N THR H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 31 removed outlier: 4.940A pdb=" N ALA H 16 " --> pdb=" O PRO H 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG H 25 " --> pdb=" O THR H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 73 through 85 removed outlier: 3.507A pdb=" N SER H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.102A pdb=" N LEU H 106 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 112 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 129 No H-bonds generated for 'chain 'H' and resid 126 through 129' Processing helix chain 'H' and resid 134 through 156 removed outlier: 4.387A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU H 150 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL H 153 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.563A pdb=" N ILE H 166 " --> pdb=" O GLN H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 191 Processing helix chain 'H' and resid 220 through 239 removed outlier: 4.291A pdb=" N TYR H 228 " --> pdb=" O PHE H 224 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 removed outlier: 3.511A pdb=" N SER H 256 " --> pdb=" O GLU H 253 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET H 260 " --> pdb=" O THR H 257 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU H 262 " --> pdb=" O PHE H 259 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU H 266 " --> pdb=" O ALA H 263 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR H 269 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG H 274 " --> pdb=" O LEU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 294 through 310 removed outlier: 4.103A pdb=" N ALA H 299 " --> pdb=" O PRO H 295 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU H 300 " --> pdb=" O LEU H 296 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE H 305 " --> pdb=" O CYS H 301 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER H 306 " --> pdb=" O MET H 302 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 19 through 25 removed outlier: 3.545A pdb=" N ALA I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 44 removed outlier: 3.787A pdb=" N MET I 38 " --> pdb=" O ARG I 34 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 39 " --> pdb=" O GLY I 35 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR I 42 " --> pdb=" O MET I 38 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 43 " --> pdb=" O THR I 39 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE I 44 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 54 No H-bonds generated for 'chain 'I' and resid 52 through 54' Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 154 through 158 Processing helix chain 'I' and resid 163 through 173 removed outlier: 3.989A pdb=" N ILE I 167 " --> pdb=" O GLU I 164 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA I 168 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE I 171 " --> pdb=" O ALA I 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 20 removed outlier: 4.119A pdb=" N LEU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 46 removed outlier: 3.681A pdb=" N GLY J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU J 41 " --> pdb=" O PHE J 37 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL J 43 " --> pdb=" O GLY J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 58 removed outlier: 3.906A pdb=" N VAL J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 73 removed outlier: 3.955A pdb=" N TYR J 69 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR J 70 " --> pdb=" O VAL J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 107 removed outlier: 3.846A pdb=" N MET J 98 " --> pdb=" O LEU J 94 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.734A pdb=" N VAL J 153 " --> pdb=" O TRP J 150 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL J 154 " --> pdb=" O MET J 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA J 155 " --> pdb=" O MET J 152 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU J 159 " --> pdb=" O GLY J 156 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE J 163 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 165 " --> pdb=" O GLY J 162 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE J 166 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE J 167 " --> pdb=" O PHE J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 20 Processing helix chain 'K' and resid 27 through 50 removed outlier: 4.500A pdb=" N GLU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU K 40 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET K 43 " --> pdb=" O SER K 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR K 47 " --> pdb=" O MET K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 82 removed outlier: 3.822A pdb=" N PHE K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU K 78 " --> pdb=" O GLY K 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 3 through 20 removed outlier: 3.628A pdb=" N LEU L 10 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE L 13 " --> pdb=" O LEU L 9 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 4.315A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 4.001A pdb=" N HIS L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 106 removed outlier: 3.863A pdb=" N LEU L 94 " --> pdb=" O THR L 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR L 97 " --> pdb=" O ALA L 93 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER L 99 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN L 102 " --> pdb=" O TRP L 98 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE L 103 " --> pdb=" O SER L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 133 removed outlier: 3.705A pdb=" N TYR L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU L 129 " --> pdb=" O LEU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 155 removed outlier: 3.640A pdb=" N GLY L 143 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL L 147 " --> pdb=" O GLY L 143 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU L 153 " --> pdb=" O ILE L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 190 removed outlier: 3.754A pdb=" N ALA L 171 " --> pdb=" O ALA L 167 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE L 180 " --> pdb=" O ARG L 176 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER L 190 " --> pdb=" O MET L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.259A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 223 removed outlier: 3.892A pdb=" N LEU L 217 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE L 218 " --> pdb=" O MET L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 237 Proline residue: L 234 - end of helix Processing helix chain 'L' and resid 241 through 250 removed outlier: 3.706A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 267 removed outlier: 4.284A pdb=" N ILE L 257 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU L 260 " --> pdb=" O GLY L 256 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL L 261 " --> pdb=" O ILE L 257 " (cutoff:3.500A) Proline residue: L 265 - end of helix Processing helix chain 'L' and resid 273 through 293 removed outlier: 4.288A pdb=" N LEU L 278 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU L 283 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR L 285 " --> pdb=" O GLY L 281 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 331 Processing helix chain 'L' and resid 333 through 349 removed outlier: 4.717A pdb=" N MET L 338 " --> pdb=" O PHE L 334 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET L 341 " --> pdb=" O ALA L 337 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER L 345 " --> pdb=" O MET L 341 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER L 349 " --> pdb=" O SER L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 369 through 381 removed outlier: 4.619A pdb=" N VAL L 374 " --> pdb=" O SER L 370 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA L 379 " --> pdb=" O ILE L 375 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 381 " --> pdb=" O SER L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 392 through 399 removed outlier: 3.745A pdb=" N ALA L 398 " --> pdb=" O LEU L 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 407 through 416 Processing helix chain 'L' and resid 418 through 429 removed outlier: 3.551A pdb=" N TYR L 422 " --> pdb=" O MET L 418 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG L 425 " --> pdb=" O MET L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.803A pdb=" N ASN L 452 " --> pdb=" O PRO L 448 " (cutoff:3.500A) Proline residue: L 453 - end of helix removed outlier: 3.731A pdb=" N ARG L 456 " --> pdb=" O ASN L 452 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA L 458 " --> pdb=" O ILE L 454 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN L 471 " --> pdb=" O VAL L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 507 removed outlier: 3.503A pdb=" N SER L 494 " --> pdb=" O ALA L 490 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA L 501 " --> pdb=" O GLY L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 522 through 525 No H-bonds generated for 'chain 'L' and resid 522 through 525' Processing helix chain 'L' and resid 529 through 533 Processing helix chain 'L' and resid 537 through 540 No H-bonds generated for 'chain 'L' and resid 537 through 540' Processing helix chain 'L' and resid 558 through 561 No H-bonds generated for 'chain 'L' and resid 558 through 561' Processing helix chain 'L' and resid 563 through 575 Processing helix chain 'L' and resid 587 through 605 removed outlier: 3.820A pdb=" N ILE L 593 " --> pdb=" O MET L 589 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN L 594 " --> pdb=" O SER L 590 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE L 604 " --> pdb=" O ILE L 600 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN L 605 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 17 removed outlier: 3.895A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix removed outlier: 3.856A pdb=" N TRP M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 37 removed outlier: 3.695A pdb=" N THR M 23 " --> pdb=" O PRO M 20 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP M 24 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR M 25 " --> pdb=" O LYS M 22 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN M 26 " --> pdb=" O THR M 23 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL M 27 " --> pdb=" O TRP M 24 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR M 30 " --> pdb=" O VAL M 27 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 42 No H-bonds generated for 'chain 'M' and resid 40 through 42' Processing helix chain 'M' and resid 60 through 78 Proline residue: M 64 - end of helix Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 removed outlier: 4.693A pdb=" N ILE M 96 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU M 102 " --> pdb=" O MET M 98 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 removed outlier: 3.506A pdb=" N LEU M 121 " --> pdb=" O MET M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 133 removed outlier: 4.063A pdb=" N ILE M 132 " --> pdb=" O PRO M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 155 removed outlier: 4.437A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR M 153 " --> pdb=" O LEU M 150 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE M 155 " --> pdb=" O TYR M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 170 Processing helix chain 'M' and resid 190 through 206 removed outlier: 3.657A pdb=" N LEU M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP M 196 " --> pdb=" O ASN M 192 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU M 197 " --> pdb=" O ASN M 193 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 220 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 226 through 233 removed outlier: 3.853A pdb=" N ILE M 230 " --> pdb=" O ALA M 226 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU M 231 " --> pdb=" O GLY M 227 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 243 Processing helix chain 'M' and resid 246 through 250 removed outlier: 3.669A pdb=" N ILE M 249 " --> pdb=" O ILE M 246 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 250 " --> pdb=" O SER M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 250' Processing helix chain 'M' and resid 259 through 275 removed outlier: 4.278A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 301 removed outlier: 4.113A pdb=" N ALA M 287 " --> pdb=" O LYS M 283 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.183A pdb=" N LEU M 315 " --> pdb=" O GLY M 311 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA M 318 " --> pdb=" O MET M 314 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU M 321 " --> pdb=" O ILE M 317 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR M 322 " --> pdb=" O ALA M 318 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS M 328 " --> pdb=" O SER M 324 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN M 333 " --> pdb=" O LEU M 329 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 366 removed outlier: 4.730A pdb=" N LEU M 360 " --> pdb=" O THR M 357 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET M 361 " --> pdb=" O TRP M 358 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER M 363 " --> pdb=" O LEU M 360 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU M 364 " --> pdb=" O MET M 361 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 388 removed outlier: 3.728A pdb=" N THR M 382 " --> pdb=" O GLU M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 392 through 415 removed outlier: 4.305A pdb=" N ILE M 398 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE M 402 " --> pdb=" O ILE M 398 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET M 405 " --> pdb=" O ILE M 401 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER M 407 " --> pdb=" O THR M 403 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET M 408 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 434 No H-bonds generated for 'chain 'M' and resid 431 through 434' Processing helix chain 'M' and resid 436 through 447 Proline residue: M 443 - end of helix Processing helix chain 'N' and resid 3 through 21 removed outlier: 4.165A pdb=" N ILE N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 28 through 44 removed outlier: 4.746A pdb=" N LEU N 33 " --> pdb=" O MET N 29 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU N 34 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE N 40 " --> pdb=" O SER N 36 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 60 removed outlier: 4.420A pdb=" N ALA N 55 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 79 removed outlier: 3.900A pdb=" N ALA N 66 " --> pdb=" O THR N 62 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER N 67 " --> pdb=" O GLN N 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA N 73 " --> pdb=" O ILE N 69 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL N 75 " --> pdb=" O LEU N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 106 removed outlier: 3.976A pdb=" N MET N 100 " --> pdb=" O ASN N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 119 Processing helix chain 'N' and resid 129 through 132 No H-bonds generated for 'chain 'N' and resid 129 through 132' Processing helix chain 'N' and resid 134 through 140 Proline residue: N 138 - end of helix No H-bonds generated for 'chain 'N' and resid 134 through 140' Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.731A pdb=" N LEU N 155 " --> pdb=" O SER N 151 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET N 156 " --> pdb=" O THR N 152 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 185 Processing helix chain 'N' and resid 188 through 195 removed outlier: 4.146A pdb=" N ILE N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU N 194 " --> pdb=" O MET N 190 " (cutoff:3.500A) Proline residue: N 195 - end of helix Processing helix chain 'N' and resid 201 through 222 removed outlier: 3.662A pdb=" N ILE N 210 " --> pdb=" O MET N 206 " (cutoff:3.500A) Proline residue: N 214 - end of helix removed outlier: 3.824A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.689A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS N 236 " --> pdb=" O LEU N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 251 removed outlier: 4.416A pdb=" N SER N 245 " --> pdb=" O THR N 242 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU N 249 " --> pdb=" O LEU N 246 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 273 Proline residue: N 262 - end of helix removed outlier: 3.576A pdb=" N ILE N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE N 266 " --> pdb=" O LYS N 263 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N MET N 271 " --> pdb=" O THR N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 300 removed outlier: 3.939A pdb=" N THR N 280 " --> pdb=" O LEU N 276 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU N 281 " --> pdb=" O ILE N 277 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET N 282 " --> pdb=" O MET N 278 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE N 291 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE N 292 " --> pdb=" O LEU N 288 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR N 293 " --> pdb=" O ASN N 289 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 314 Processing helix chain 'N' and resid 327 through 330 No H-bonds generated for 'chain 'N' and resid 327 through 330' Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 6 through 10 Processing helix chain 'O' and resid 43 through 46 No H-bonds generated for 'chain 'O' and resid 43 through 46' Processing helix chain 'O' and resid 60 through 62 No H-bonds generated for 'chain 'O' and resid 60 through 62' Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.674A pdb=" N TYR O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 79 through 84' Processing helix chain 'O' and resid 95 through 115 removed outlier: 3.707A pdb=" N LEU O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER O 103 " --> pdb=" O TRP O 99 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU O 112 " --> pdb=" O TYR O 108 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 140 removed outlier: 4.831A pdb=" N PHE O 132 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU O 136 " --> pdb=" O VAL O 133 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA O 137 " --> pdb=" O PHE O 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN O 140 " --> pdb=" O ALA O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 159 removed outlier: 3.611A pdb=" N ASP O 150 " --> pdb=" O LYS O 146 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS O 151 " --> pdb=" O GLN O 147 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR O 152 " --> pdb=" O CYS O 148 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE O 155 " --> pdb=" O HIS O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 184 removed outlier: 3.976A pdb=" N SER O 181 " --> pdb=" O PRO O 177 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN O 184 " --> pdb=" O GLN O 180 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 217 removed outlier: 4.788A pdb=" N GLU O 203 " --> pdb=" O LEU O 199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA O 205 " --> pdb=" O ASP O 201 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS O 208 " --> pdb=" O ASN O 204 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix removed outlier: 3.809A pdb=" N GLU O 216 " --> pdb=" O PRO O 212 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET O 217 " --> pdb=" O LYS O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 231 through 239 removed outlier: 3.600A pdb=" N GLU O 239 " --> pdb=" O VAL O 235 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 249 No H-bonds generated for 'chain 'O' and resid 247 through 249' Processing helix chain 'O' and resid 253 through 263 removed outlier: 3.618A pdb=" N LEU O 262 " --> pdb=" O TYR O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 297 removed outlier: 3.903A pdb=" N ILE O 292 " --> pdb=" O GLN O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 312 No H-bonds generated for 'chain 'O' and resid 310 through 312' Processing helix chain 'P' and resid 30 through 39 Processing helix chain 'P' and resid 54 through 59 removed outlier: 3.608A pdb=" N MET P 57 " --> pdb=" O TYR P 54 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 85 Processing helix chain 'P' and resid 106 through 110 Processing helix chain 'P' and resid 112 through 123 Processing helix chain 'P' and resid 145 through 157 removed outlier: 4.094A pdb=" N LYS P 149 " --> pdb=" O SER P 145 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL P 151 " --> pdb=" O ARG P 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY P 152 " --> pdb=" O SER P 148 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG P 157 " --> pdb=" O GLU P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 179 through 184 Processing helix chain 'P' and resid 207 through 217 removed outlier: 4.212A pdb=" N GLY P 213 " --> pdb=" O ASP P 209 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 249 removed outlier: 3.563A pdb=" N LYS P 243 " --> pdb=" O PHE P 239 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 288 removed outlier: 3.517A pdb=" N ARG P 286 " --> pdb=" O ASP P 282 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS P 288 " --> pdb=" O VAL P 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 321 removed outlier: 4.841A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 31 No H-bonds generated for 'chain 'Q' and resid 28 through 31' Processing helix chain 'Q' and resid 89 through 99 removed outlier: 3.527A pdb=" N ILE Q 93 " --> pdb=" O LYS Q 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA Q 94 " --> pdb=" O GLU Q 90 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN Q 99 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 122 Processing helix chain 'R' and resid 23 through 28 Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.930A pdb=" N ALA R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 46 removed outlier: 3.779A pdb=" N VAL S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL S 41 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU S 42 " --> pdb=" O GLN S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 91 Processing helix chain 'T' and resid 9 through 20 removed outlier: 3.611A pdb=" N LEU T 16 " --> pdb=" O LYS T 12 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR T 17 " --> pdb=" O ASP T 13 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL T 18 " --> pdb=" O ARG T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 58 removed outlier: 3.616A pdb=" N ILE T 50 " --> pdb=" O ASP T 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET T 52 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA T 53 " --> pdb=" O GLU T 49 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET T 54 " --> pdb=" O ILE T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 69 No H-bonds generated for 'chain 'T' and resid 67 through 69' Processing helix chain 'T' and resid 75 through 81 removed outlier: 3.519A pdb=" N ALA T 81 " --> pdb=" O VAL T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 12 through 21 removed outlier: 4.029A pdb=" N TYR U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU U 21 " --> pdb=" O TYR U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 58 removed outlier: 3.582A pdb=" N GLU U 49 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE U 50 " --> pdb=" O ASP U 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET U 52 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA U 53 " --> pdb=" O GLU U 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET U 54 " --> pdb=" O ILE U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 73 through 84 removed outlier: 3.703A pdb=" N ALA U 81 " --> pdb=" O VAL U 77 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP U 82 " --> pdb=" O ASP U 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 22 through 33 Processing helix chain 'V' and resid 44 through 58 removed outlier: 3.940A pdb=" N GLU V 48 " --> pdb=" O ARG V 44 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN V 49 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 67 No H-bonds generated for 'chain 'V' and resid 64 through 67' Processing helix chain 'V' and resid 76 through 95 removed outlier: 3.704A pdb=" N LEU V 89 " --> pdb=" O LYS V 85 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG V 91 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 43 removed outlier: 4.991A pdb=" N ARG W 32 " --> pdb=" O ASN W 28 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG W 33 " --> pdb=" O GLU W 29 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG W 35 " --> pdb=" O LYS W 31 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA W 40 " --> pdb=" O GLU W 36 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ARG W 43 " --> pdb=" O ARG W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 46 through 51 removed outlier: 3.526A pdb=" N HIS W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 69 Processing helix chain 'W' and resid 78 through 95 removed outlier: 4.376A pdb=" N ILE W 86 " --> pdb=" O ASP W 82 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 12 No H-bonds generated for 'chain 'X' and resid 10 through 12' Processing helix chain 'X' and resid 22 through 33 removed outlier: 3.626A pdb=" N ALA X 27 " --> pdb=" O VAL X 23 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA X 28 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS X 29 " --> pdb=" O LYS X 25 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N HIS X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 48 removed outlier: 3.626A pdb=" N GLU X 41 " --> pdb=" O LYS X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 74 removed outlier: 3.630A pdb=" N ASN X 68 " --> pdb=" O GLY X 64 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE X 73 " --> pdb=" O PHE X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 88 removed outlier: 3.725A pdb=" N THR X 86 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS X 87 " --> pdb=" O GLU X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 111 removed outlier: 3.912A pdb=" N LYS X 105 " --> pdb=" O GLN X 101 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS X 109 " --> pdb=" O LYS X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 124 No H-bonds generated for 'chain 'X' and resid 122 through 124' Processing helix chain 'Y' and resid 2 through 8 removed outlier: 3.505A pdb=" N GLU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR Y 8 " --> pdb=" O PHE Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 41 removed outlier: 4.043A pdb=" N TYR Y 22 " --> pdb=" O HIS Y 18 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N CYS Y 31 " --> pdb=" O LEU Y 27 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER Y 36 " --> pdb=" O GLY Y 32 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER Y 39 " --> pdb=" O GLY Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 78 removed outlier: 3.915A pdb=" N ARG Y 54 " --> pdb=" O GLU Y 50 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA Y 64 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE Y 69 " --> pdb=" O ILE Y 65 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR Y 72 " --> pdb=" O MET Y 68 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 103 removed outlier: 3.980A pdb=" N ILE Y 91 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Y 92 " --> pdb=" O TYR Y 89 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY Y 93 " --> pdb=" O PHE Y 90 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS Y 94 " --> pdb=" O ILE Y 91 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU Y 98 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY Y 101 " --> pdb=" O LEU Y 98 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG Y 103 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 114 Processing helix chain 'Y' and resid 116 through 130 removed outlier: 3.706A pdb=" N ALA Y 121 " --> pdb=" O MET Y 117 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Y 122 " --> pdb=" O GLY Y 118 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY Y 127 " --> pdb=" O LEU Y 123 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS Y 128 " --> pdb=" O PHE Y 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 32 through 48 removed outlier: 4.310A pdb=" N VAL Z 37 " --> pdb=" O SER Z 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE Z 44 " --> pdb=" O GLY Z 40 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR Z 46 " --> pdb=" O LEU Z 42 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG Z 48 " --> pdb=" O PHE Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 50 through 64 removed outlier: 4.414A pdb=" N GLU Z 55 " --> pdb=" O ARG Z 51 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU Z 62 " --> pdb=" O ARG Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 93 removed outlier: 3.545A pdb=" N ALA Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU Z 83 " --> pdb=" O ASP Z 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU Z 86 " --> pdb=" O THR Z 82 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU Z 92 " --> pdb=" O GLU Z 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 135 No H-bonds generated for 'chain 'Z' and resid 132 through 135' Processing helix chain 'Z' and resid 139 through 141 No H-bonds generated for 'chain 'Z' and resid 139 through 141' Processing helix chain 'a' and resid 6 through 14 removed outlier: 3.920A pdb=" N ILE a 11 " --> pdb=" O PRO a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 31 removed outlier: 3.787A pdb=" N GLY a 20 " --> pdb=" O LEU a 16 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 54 removed outlier: 3.681A pdb=" N LEU a 47 " --> pdb=" O TYR a 43 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET a 48 " --> pdb=" O GLN a 44 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE a 54 " --> pdb=" O ARG a 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 14 removed outlier: 3.993A pdb=" N PHE b 7 " --> pdb=" O ARG b 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 34 removed outlier: 3.582A pdb=" N GLY b 26 " --> pdb=" O PHE b 22 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE b 29 " --> pdb=" O TRP b 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE b 30 " --> pdb=" O GLY b 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET b 31 " --> pdb=" O LEU b 27 " (cutoff:3.500A) Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 37 through 46 removed outlier: 3.604A pdb=" N SER b 42 " --> pdb=" O LYS b 39 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET b 43 " --> pdb=" O TYR b 40 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE b 44 " --> pdb=" O ALA b 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 14 through 45 removed outlier: 3.740A pdb=" N GLY c 18 " --> pdb=" O TRP c 14 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU c 19 " --> pdb=" O LEU c 15 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY c 22 " --> pdb=" O GLY c 18 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE c 26 " --> pdb=" O GLY c 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU c 31 " --> pdb=" O MET c 27 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG c 44 " --> pdb=" O LEU c 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 31 through 48 removed outlier: 3.587A pdb=" N MET d 44 " --> pdb=" O CYS d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 95 removed outlier: 3.932A pdb=" N VAL d 69 " --> pdb=" O VAL d 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR d 81 " --> pdb=" O LYS d 77 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET d 90 " --> pdb=" O LYS d 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY d 92 " --> pdb=" O HIS d 88 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 8 No H-bonds generated for 'chain 'e' and resid 5 through 8' Processing helix chain 'e' and resid 33 through 42 removed outlier: 3.629A pdb=" N CYS e 42 " --> pdb=" O GLU e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 51 No H-bonds generated for 'chain 'e' and resid 49 through 51' Processing helix chain 'e' and resid 56 through 66 removed outlier: 3.566A pdb=" N GLU e 64 " --> pdb=" O ASP e 60 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 85 removed outlier: 3.624A pdb=" N ARG e 73 " --> pdb=" O TYR e 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE e 78 " --> pdb=" O ARG e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 97 No H-bonds generated for 'chain 'e' and resid 95 through 97' Processing helix chain 'f' and resid 11 through 33 removed outlier: 4.469A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix removed outlier: 3.799A pdb=" N VAL f 20 " --> pdb=" O ALA f 17 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY f 22 " --> pdb=" O PHE f 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP f 26 " --> pdb=" O CYS f 23 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP f 29 " --> pdb=" O ASP f 26 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU f 31 " --> pdb=" O LYS f 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 63 removed outlier: 4.095A pdb=" N VAL g 53 " --> pdb=" O PRO g 49 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TRP g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA g 58 " --> pdb=" O TRP g 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 76 removed outlier: 3.872A pdb=" N PHE g 74 " --> pdb=" O PHE g 70 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA g 76 " --> pdb=" O THR g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 101 removed outlier: 3.975A pdb=" N ARG g 89 " --> pdb=" O GLU g 85 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL g 100 " --> pdb=" O LYS g 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN g 101 " --> pdb=" O TYR g 97 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 46 removed outlier: 3.555A pdb=" N PHE h 21 " --> pdb=" O TYR h 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE h 27 " --> pdb=" O ARG h 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU h 29 " --> pdb=" O MET h 25 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET h 30 " --> pdb=" O LYS h 26 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix removed outlier: 3.661A pdb=" N ASN h 44 " --> pdb=" O ILE h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.483A pdb=" N ARG h 77 " --> pdb=" O ARG h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 116 removed outlier: 4.267A pdb=" N GLU h 88 " --> pdb=" O GLU h 84 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS h 89 " --> pdb=" O LYS h 85 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU h 91 " --> pdb=" O TYR h 87 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU h 99 " --> pdb=" O GLN h 95 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS h 100 " --> pdb=" O ILE h 96 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA h 101 " --> pdb=" O GLU h 97 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG h 115 " --> pdb=" O ARG h 111 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA h 116 " --> pdb=" O ARG h 112 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 132 No H-bonds generated for 'chain 'h' and resid 130 through 132' Processing helix chain 'i' and resid 5 through 22 removed outlier: 4.049A pdb=" N LEU i 14 " --> pdb=" O ARG i 10 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU i 16 " --> pdb=" O GLN i 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG i 20 " --> pdb=" O GLU i 16 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP i 21 " --> pdb=" O LEU i 17 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 74 removed outlier: 4.034A pdb=" N SER i 67 " --> pdb=" O TYR i 64 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU i 68 " --> pdb=" O ARG i 65 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA i 70 " --> pdb=" O SER i 67 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL i 71 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL i 74 " --> pdb=" O VAL i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 88 removed outlier: 3.838A pdb=" N TYR i 87 " --> pdb=" O TYR i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 21 through 38 removed outlier: 4.263A pdb=" N TRP j 33 " --> pdb=" O SER j 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 38 through 41 No H-bonds generated for 'chain 'k' and resid 38 through 41' Processing helix chain 'k' and resid 53 through 55 No H-bonds generated for 'chain 'k' and resid 53 through 55' Processing helix chain 'k' and resid 68 through 70 No H-bonds generated for 'chain 'k' and resid 68 through 70' Processing helix chain 'k' and resid 76 through 88 removed outlier: 3.566A pdb=" N ALA k 86 " --> pdb=" O ALA k 82 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 7 No H-bonds generated for 'chain 'l' and resid 5 through 7' Processing helix chain 'l' and resid 18 through 23 removed outlier: 3.574A pdb=" N ALA l 23 " --> pdb=" O ALA l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 97 through 120 removed outlier: 3.865A pdb=" N LEU l 104 " --> pdb=" O MET l 100 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE l 105 " --> pdb=" O CYS l 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE l 113 " --> pdb=" O ALA l 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET l 114 " --> pdb=" O PHE l 110 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE l 115 " --> pdb=" O MET l 111 " (cutoff:3.500A) Processing helix chain 'm' and resid 29 through 50 removed outlier: 4.061A pdb=" N LEU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU m 42 " --> pdb=" O ILE m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 76 through 78 No H-bonds generated for 'chain 'm' and resid 76 through 78' Processing helix chain 'm' and resid 86 through 93 removed outlier: 3.609A pdb=" N ALA m 90 " --> pdb=" O SER m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 95 through 115 removed outlier: 4.042A pdb=" N TYR m 101 " --> pdb=" O LEU m 97 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR m 102 " --> pdb=" O ILE m 98 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL m 103 " --> pdb=" O PHE m 99 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS m 105 " --> pdb=" O TYR m 101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG m 113 " --> pdb=" O ASP m 109 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU m 114 " --> pdb=" O ARG m 110 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 27 removed outlier: 3.704A pdb=" N LEU n 26 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU n 27 " --> pdb=" O LEU n 23 " (cutoff:3.500A) Processing helix chain 'n' and resid 33 through 48 removed outlier: 3.564A pdb=" N TYR n 38 " --> pdb=" O ASP n 34 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE n 39 " --> pdb=" O LYS n 35 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA n 40 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS n 41 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 63 Processing helix chain 'n' and resid 65 through 70 Processing helix chain 'n' and resid 92 through 94 No H-bonds generated for 'chain 'n' and resid 92 through 94' Processing helix chain 'n' and resid 102 through 105 Processing helix chain 'n' and resid 117 through 141 removed outlier: 3.798A pdb=" N GLN n 123 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU n 127 " --> pdb=" O GLN n 123 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU n 139 " --> pdb=" O GLU n 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 43 through 48 removed outlier: 3.561A pdb=" N ASP o 47 " --> pdb=" O GLN o 43 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA o 48 " --> pdb=" O GLU o 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 43 through 48' Processing helix chain 'o' and resid 59 through 67 removed outlier: 3.683A pdb=" N ARG o 64 " --> pdb=" O HIS o 60 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 114 removed outlier: 3.879A pdb=" N TRP o 86 " --> pdb=" O GLU o 82 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG o 114 " --> pdb=" O ARG o 110 " (cutoff:3.500A) Processing helix chain 'p' and resid 30 through 33 No H-bonds generated for 'chain 'p' and resid 30 through 33' Processing helix chain 'p' and resid 41 through 55 removed outlier: 4.098A pdb=" N ARG p 53 " --> pdb=" O GLU p 49 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN p 54 " --> pdb=" O PHE p 50 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 115 removed outlier: 3.595A pdb=" N LYS p 96 " --> pdb=" O ARG p 92 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN p 99 " --> pdb=" O PHE p 95 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE p 101 " --> pdb=" O VAL p 97 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET p 102 " --> pdb=" O ASP p 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA p 111 " --> pdb=" O GLU p 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS p 112 " --> pdb=" O ARG p 108 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN p 113 " --> pdb=" O LEU p 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 141 removed outlier: 3.519A pdb=" N VAL p 134 " --> pdb=" O GLN p 130 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA p 137 " --> pdb=" O LYS p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 151 through 170 removed outlier: 3.568A pdb=" N MET p 162 " --> pdb=" O GLN p 158 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU p 163 " --> pdb=" O LYS p 159 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU p 164 " --> pdb=" O GLN p 160 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA p 169 " --> pdb=" O GLU p 165 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG p 170 " --> pdb=" O ARG p 166 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 removed outlier: 3.603A pdb=" N LEU q 7 " --> pdb=" O LEU q 3 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 16 No H-bonds generated for 'chain 'q' and resid 14 through 16' Processing helix chain 'q' and resid 21 through 30 removed outlier: 3.871A pdb=" N VAL q 26 " --> pdb=" O GLY q 22 " (cutoff:3.500A) Processing helix chain 'q' and resid 87 through 90 No H-bonds generated for 'chain 'q' and resid 87 through 90' Processing helix chain 'r' and resid 7 through 15 Processing helix chain 's' and resid 44 through 55 removed outlier: 3.536A pdb=" N LEU s 48 " --> pdb=" O THR s 44 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN s 49 " --> pdb=" O PHE s 45 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP s 51 " --> pdb=" O ASP s 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER s 53 " --> pdb=" O ASN s 49 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS s 54 " --> pdb=" O LEU s 50 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE s 55 " --> pdb=" O ASP s 51 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.552A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 77 through 82 removed outlier: 4.012A pdb=" N ASP C 77 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN C 95 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 93 " --> pdb=" O THR C 79 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 96 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 105 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 173 through 177 removed outlier: 3.552A pdb=" N GLU C 173 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP C 177 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.657A pdb=" N GLN E 101 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 222 through 224 removed outlier: 8.155A pdb=" N ALA F 223 " --> pdb=" O TYR F 92 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL F 94 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA F 133 " --> pdb=" O LEU F 93 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N VAL F 95 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR F 135 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 257 through 259 Processing sheet with id= G, first strand: chain 'G' and resid 18 through 20 removed outlier: 5.902A pdb=" N TRP G 77 " --> pdb=" O PHE G 12 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= I, first strand: chain 'G' and resid 223 through 228 removed outlier: 3.550A pdb=" N ARG G 223 " --> pdb=" O THR G 242 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR G 242 " --> pdb=" O ARG G 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER G 241 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG G 249 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 283 through 285 Processing sheet with id= K, first strand: chain 'G' and resid 315 through 318 removed outlier: 6.445A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 405 through 408 removed outlier: 6.797A pdb=" N ASN G 491 " --> pdb=" O LEU G 453 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 544 through 547 removed outlier: 5.860A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'I' and resid 66 through 69 Processing sheet with id= O, first strand: chain 'I' and resid 98 through 100 removed outlier: 3.530A pdb=" N ARG I 107 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 21 through 23 removed outlier: 3.759A pdb=" N VAL P 23 " --> pdb=" O ILE P 46 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR P 69 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU P 71 " --> pdb=" O ILE P 47 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 90 through 93 removed outlier: 6.397A pdb=" N ARG P 128 " --> pdb=" O VAL P 91 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN P 93 " --> pdb=" O ARG P 128 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE P 130 " --> pdb=" O ASN P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'Q' and resid 34 through 37 removed outlier: 6.557A pdb=" N SER Q 102 " --> pdb=" O VAL Q 35 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE Q 37 " --> pdb=" O SER Q 102 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP Q 104 " --> pdb=" O ILE Q 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'Q' and resid 64 through 66 Processing sheet with id= T, first strand: chain 'R' and resid 56 through 58 removed outlier: 4.127A pdb=" N ILE R 57 " --> pdb=" O ILE R 73 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE R 73 " --> pdb=" O ILE R 57 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= V, first strand: chain 'S' and resid 65 through 67 removed outlier: 3.606A pdb=" N ALA S 66 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS S 74 " --> pdb=" O ALA S 66 " (cutoff:3.500A) No H-bonds generated for sheet with id= V 1778 hydrogen bonds defined for protein. 4821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.00 Time building geometry restraints manager: 23.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27078 1.40 - 1.62: 38616 1.62 - 1.85: 803 1.85 - 2.07: 0 2.07 - 2.29: 80 Bond restraints: 66577 Sorted by residual: bond pdb=" CA AME q 1 " pdb=" C AME q 1 " ideal model delta sigma weight residual 1.527 1.319 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" NE 2MR D 85 " pdb=" CZ 2MR D 85 " ideal model delta sigma weight residual 1.371 1.453 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C AME q 1 " pdb=" O AME q 1 " ideal model delta sigma weight residual 1.259 1.179 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" CA PRO D 359 " pdb=" C PRO D 359 " ideal model delta sigma weight residual 1.517 1.496 0.021 6.70e-03 2.23e+04 9.99e+00 bond pdb=" CZ 2MR D 85 " pdb=" NH2 2MR D 85 " ideal model delta sigma weight residual 1.385 1.448 -0.063 2.00e-02 2.50e+03 9.99e+00 ... (remaining 66572 not shown) Histogram of bond angle deviations from ideal: 72.19 - 84.98: 76 84.98 - 97.77: 26 97.77 - 110.55: 20937 110.55 - 123.34: 65567 123.34 - 136.13: 3723 Bond angle restraints: 90329 Sorted by residual: angle pdb=" N ILE E 100 " pdb=" CA ILE E 100 " pdb=" C ILE E 100 " ideal model delta sigma weight residual 106.21 110.96 -4.75 1.07e+00 8.73e-01 1.97e+01 angle pdb=" N ILE I 26 " pdb=" CA ILE I 26 " pdb=" C ILE I 26 " ideal model delta sigma weight residual 109.34 100.15 9.19 2.08e+00 2.31e-01 1.95e+01 angle pdb=" CA VAL q 82 " pdb=" CB VAL q 82 " pdb=" CG2 VAL q 82 " ideal model delta sigma weight residual 110.40 117.89 -7.49 1.70e+00 3.46e-01 1.94e+01 angle pdb=" C SER K 56 " pdb=" N MET K 57 " pdb=" CA MET K 57 " ideal model delta sigma weight residual 120.06 125.26 -5.20 1.19e+00 7.06e-01 1.91e+01 angle pdb=" C ASP U 2 " pdb=" CA ASP U 2 " pdb=" CB ASP U 2 " ideal model delta sigma weight residual 116.53 110.15 6.38 1.47e+00 4.63e-01 1.88e+01 ... (remaining 90324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 39510 33.98 - 67.97: 421 67.97 - 101.95: 40 101.95 - 135.94: 4 135.94 - 169.92: 3 Dihedral angle restraints: 39978 sinusoidal: 16437 harmonic: 23541 Sorted by residual: dihedral pdb=" CA ILE G 258 " pdb=" C ILE G 258 " pdb=" N ASN G 259 " pdb=" CA ASN G 259 " ideal model delta harmonic sigma weight residual -180.00 -115.10 -64.90 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" CA TYR a 61 " pdb=" C TYR a 61 " pdb=" N VAL a 62 " pdb=" CA VAL a 62 " ideal model delta harmonic sigma weight residual -180.00 -127.50 -52.50 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CA ILE I 26 " pdb=" C ILE I 26 " pdb=" N LEU I 27 " pdb=" CA LEU I 27 " ideal model delta harmonic sigma weight residual -180.00 -129.59 -50.41 0 5.00e+00 4.00e-02 1.02e+02 ... (remaining 39975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.217: 9950 4.217 - 8.434: 0 8.434 - 12.651: 0 12.651 - 16.868: 0 16.868 - 21.085: 24 Chirality restraints: 9974 Sorted by residual: chirality pdb="FE3 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S2 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.09 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.52 21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.49 21.05 2.00e-01 2.50e+01 1.11e+04 ... (remaining 9971 not shown) Planarity restraints: 11402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG f 48 " -0.095 5.00e-02 4.00e+02 1.47e-01 3.46e+01 pdb=" N PRO f 49 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO f 49 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO f 49 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 206 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO F 207 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 598 " 0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE L 598 " -0.063 2.00e-02 2.50e+03 pdb=" O ILE L 598 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE L 599 " 0.021 2.00e-02 2.50e+03 ... (remaining 11399 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 59 2.16 - 2.84: 22553 2.84 - 3.53: 96649 3.53 - 4.21: 156869 4.21 - 4.90: 261797 Nonbonded interactions: 537927 Sorted by model distance: nonbonded pdb=" OXT AME q 1 " pdb=" CA GLU q 2 " model vdw 1.475 2.776 nonbonded pdb=" O GLU R 34 " pdb=" OH TYR q 127 " model vdw 1.983 2.440 nonbonded pdb=" OE2 GLU T 49 " pdb=" OH TYR W 38 " model vdw 1.987 2.440 nonbonded pdb=" OH TYR i 94 " pdb=" O LYS p 6 " model vdw 2.002 2.440 nonbonded pdb=" O LEU M 179 " pdb=" OG1 THR M 183 " model vdw 2.009 2.440 ... (remaining 537922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 8 through 82 or (resid 201 and (name C1 or name C10 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or \ name C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 or \ name N2 or name O1 or name O2 or name O3 or name O4 or name O5 or name O6 or nam \ e O7 or name O9 or name P1 or name S1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.340 Check model and map are aligned: 0.810 Set scattering table: 0.430 Process input model: 146.910 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.208 66577 Z= 0.743 Angle : 1.102 12.902 90329 Z= 0.583 Chirality : 1.031 21.085 9974 Planarity : 0.007 0.147 11402 Dihedral : 11.755 169.921 24744 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.44 % Allowed : 16.83 % Favored : 82.73 % Rotamer: Outliers : 0.23 % Allowed : 6.17 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.52 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.65 (0.07), residues: 7951 helix: -3.73 (0.06), residues: 3495 sheet: -4.16 (0.20), residues: 369 loop : -3.79 (0.09), residues: 4087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 98 HIS 0.019 0.003 HIS F 261 PHE 0.036 0.003 PHE N 305 TYR 0.043 0.003 TYR a 61 ARG 0.018 0.002 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2521 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 2505 time to evaluate : 5.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 VAL cc_start: 0.7867 (m) cc_final: 0.7654 (t) REVERT: B 44 ASP cc_start: 0.8114 (t70) cc_final: 0.7905 (t0) REVERT: B 48 ASN cc_start: 0.8620 (m-40) cc_final: 0.8323 (m110) REVERT: B 79 MET cc_start: 0.8291 (mtm) cc_final: 0.8086 (mtp) REVERT: B 126 MET cc_start: 0.7802 (ttm) cc_final: 0.7416 (mtp) REVERT: C 77 ASP cc_start: 0.7910 (m-30) cc_final: 0.7481 (m-30) REVERT: C 137 MET cc_start: 0.8927 (mmp) cc_final: 0.8675 (mmm) REVERT: C 174 LEU cc_start: 0.8731 (mp) cc_final: 0.8526 (mp) REVERT: D 23 LYS cc_start: 0.7977 (ptpp) cc_final: 0.7200 (tttp) REVERT: D 72 MET cc_start: 0.7177 (tpp) cc_final: 0.6787 (tpp) REVERT: D 157 HIS cc_start: 0.8612 (t-90) cc_final: 0.8298 (t70) REVERT: D 168 PHE cc_start: 0.8571 (m-80) cc_final: 0.8084 (m-80) REVERT: D 189 MET cc_start: 0.7881 (ttt) cc_final: 0.7561 (ttt) REVERT: D 200 HIS cc_start: 0.5644 (t-90) cc_final: 0.5225 (t70) REVERT: D 219 SER cc_start: 0.8290 (t) cc_final: 0.7821 (t) REVERT: D 338 MET cc_start: 0.8673 (ppp) cc_final: 0.8050 (ppp) REVERT: E 55 GLN cc_start: 0.8878 (tp40) cc_final: 0.8658 (tp-100) REVERT: E 82 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6782 (mm-30) REVERT: E 93 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8324 (mmmt) REVERT: E 99 HIS cc_start: 0.7428 (t-90) cc_final: 0.7088 (t-90) REVERT: E 174 ASP cc_start: 0.6951 (m-30) cc_final: 0.6476 (t0) REVERT: F 110 ILE cc_start: 0.8367 (tp) cc_final: 0.8157 (tp) REVERT: F 114 ASP cc_start: 0.7895 (p0) cc_final: 0.7631 (p0) REVERT: F 218 CYS cc_start: 0.7417 (m) cc_final: 0.7208 (m) REVERT: F 390 ASP cc_start: 0.7243 (p0) cc_final: 0.6995 (p0) REVERT: F 395 ILE cc_start: 0.8407 (mp) cc_final: 0.8123 (mm) REVERT: G 71 MET cc_start: 0.8470 (tpt) cc_final: 0.8090 (tpt) REVERT: G 74 MET cc_start: 0.7640 (mtp) cc_final: 0.7325 (mtt) REVERT: G 94 MET cc_start: 0.7467 (mmm) cc_final: 0.7227 (mmm) REVERT: G 95 GLU cc_start: 0.8604 (tt0) cc_final: 0.8280 (tt0) REVERT: G 414 ASP cc_start: 0.7605 (p0) cc_final: 0.7179 (t70) REVERT: G 430 GLN cc_start: 0.7231 (mt0) cc_final: 0.7019 (tm-30) REVERT: G 491 ASN cc_start: 0.5531 (p0) cc_final: 0.5125 (p0) REVERT: G 504 ASP cc_start: 0.8594 (m-30) cc_final: 0.8288 (t0) REVERT: G 521 MET cc_start: 0.7461 (tmm) cc_final: 0.7172 (tmm) REVERT: G 622 ARG cc_start: 0.7310 (tpt170) cc_final: 0.7002 (tpt170) REVERT: H 35 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8602 (mttm) REVERT: H 57 MET cc_start: 0.7298 (mtt) cc_final: 0.7056 (mtt) REVERT: H 85 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8950 (tm) REVERT: H 146 MET cc_start: 0.7978 (mtp) cc_final: 0.6409 (ttt) REVERT: H 161 SER cc_start: 0.8727 (t) cc_final: 0.8468 (p) REVERT: I 7 LYS cc_start: 0.6560 (tmtp) cc_final: 0.6352 (tmtt) REVERT: I 49 THR cc_start: 0.8842 (p) cc_final: 0.8546 (p) REVERT: I 51 ASN cc_start: 0.7890 (m-40) cc_final: 0.7617 (m110) REVERT: I 109 THR cc_start: 0.8467 (p) cc_final: 0.8264 (p) REVERT: I 125 GLN cc_start: 0.8151 (pt0) cc_final: 0.7821 (pt0) REVERT: I 174 ASP cc_start: 0.7652 (t70) cc_final: 0.7288 (t0) REVERT: J 63 MET cc_start: 0.7533 (mpt) cc_final: 0.7217 (mpt) REVERT: J 152 MET cc_start: 0.8849 (tpt) cc_final: 0.8510 (tpp) REVERT: K 83 ASN cc_start: 0.8459 (m-40) cc_final: 0.8116 (m110) REVERT: K 92 ASN cc_start: 0.7696 (t160) cc_final: 0.7004 (t0) REVERT: K 96 LEU cc_start: 0.7859 (mt) cc_final: 0.7644 (mp) REVERT: K 97 GLN cc_start: 0.8166 (pp30) cc_final: 0.7293 (pp30) REVERT: L 59 MET cc_start: 0.7573 (mmm) cc_final: 0.7351 (mmm) REVERT: L 226 GLN cc_start: 0.6808 (mm-40) cc_final: 0.6497 (mm-40) REVERT: L 261 VAL cc_start: 0.7901 (m) cc_final: 0.7641 (p) REVERT: L 352 ASP cc_start: 0.6307 (t70) cc_final: 0.5869 (t0) REVERT: L 587 TYR cc_start: 0.9163 (m-10) cc_final: 0.8174 (m-10) REVERT: M 267 TRP cc_start: 0.7856 (t-100) cc_final: 0.7609 (t-100) REVERT: M 310 MET cc_start: 0.7226 (ttt) cc_final: 0.5932 (ttt) REVERT: M 313 THR cc_start: 0.9036 (p) cc_final: 0.8635 (p) REVERT: M 442 ILE cc_start: 0.8416 (mp) cc_final: 0.8122 (mt) REVERT: M 454 ILE cc_start: 0.9200 (tp) cc_final: 0.8991 (tt) REVERT: M 459 MET cc_start: 0.6441 (mmp) cc_final: 0.5736 (mmt) REVERT: N 26 LEU cc_start: 0.9097 (mt) cc_final: 0.8834 (mt) REVERT: N 126 MET cc_start: 0.6618 (tpp) cc_final: 0.5430 (tpp) REVERT: N 197 ASN cc_start: 0.8239 (t0) cc_final: 0.7426 (t0) REVERT: O 13 LYS cc_start: 0.7367 (mmtt) cc_final: 0.7014 (mmtp) REVERT: O 96 LEU cc_start: 0.8974 (tp) cc_final: 0.8742 (tt) REVERT: O 165 PRO cc_start: 0.8326 (Cg_endo) cc_final: 0.7588 (Cg_exo) REVERT: O 225 SER cc_start: 0.7651 (p) cc_final: 0.7081 (m) REVERT: O 261 MET cc_start: 0.7924 (mmm) cc_final: 0.7517 (mmm) REVERT: O 265 ASP cc_start: 0.6767 (m-30) cc_final: 0.6460 (m-30) REVERT: P 82 ARG cc_start: 0.8356 (tpt-90) cc_final: 0.7810 (tmm160) REVERT: P 98 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7330 (mp0) REVERT: Q 38 PHE cc_start: 0.8787 (p90) cc_final: 0.8497 (p90) REVERT: Q 39 VAL cc_start: 0.8820 (t) cc_final: 0.8463 (m) REVERT: Q 80 SER cc_start: 0.8157 (p) cc_final: 0.7955 (m) REVERT: R 36 ASN cc_start: 0.7955 (t0) cc_final: 0.7685 (m-40) REVERT: R 42 ASP cc_start: 0.8095 (m-30) cc_final: 0.7808 (m-30) REVERT: R 73 ILE cc_start: 0.8736 (mp) cc_final: 0.8373 (mp) REVERT: S 86 VAL cc_start: 0.8684 (t) cc_final: 0.8450 (p) REVERT: T 20 LYS cc_start: 0.7986 (pttp) cc_final: 0.7341 (tptt) REVERT: U 62 ILE cc_start: 0.6276 (mm) cc_final: 0.6075 (mm) REVERT: U 74 GLN cc_start: 0.8155 (tp40) cc_final: 0.7873 (tm-30) REVERT: V 82 GLN cc_start: 0.8233 (tp40) cc_final: 0.7906 (tp40) REVERT: V 110 GLN cc_start: 0.7242 (tm-30) cc_final: 0.6601 (tm-30) REVERT: X 53 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.5956 (mtm180) REVERT: Y 2 LYS cc_start: 0.6248 (tptt) cc_final: 0.6046 (ptpp) REVERT: Y 107 TYR cc_start: 0.6374 (m-10) cc_final: 0.6150 (p90) REVERT: Z 102 ASN cc_start: 0.5503 (p0) cc_final: 0.5271 (t0) REVERT: a 47 LEU cc_start: 0.8546 (mt) cc_final: 0.8162 (mp) REVERT: b 15 GLU cc_start: 0.7013 (tt0) cc_final: 0.6733 (tt0) REVERT: b 33 MET cc_start: 0.7364 (mtp) cc_final: 0.7043 (mtp) REVERT: d 2 MET cc_start: 0.8111 (mmm) cc_final: 0.7811 (mmp) REVERT: d 3 ASN cc_start: 0.8457 (p0) cc_final: 0.7998 (m-40) REVERT: d 25 LYS cc_start: 0.7926 (ttmp) cc_final: 0.7594 (tttp) REVERT: d 36 LEU cc_start: 0.8077 (mt) cc_final: 0.7792 (tt) REVERT: d 109 TYR cc_start: 0.8168 (m-80) cc_final: 0.7322 (m-80) REVERT: e 26 TYR cc_start: 0.5785 (m-10) cc_final: 0.5406 (m-10) REVERT: g 96 LYS cc_start: 0.8810 (ptmm) cc_final: 0.8539 (pttp) REVERT: g 118 LEU cc_start: 0.8490 (mp) cc_final: 0.8210 (mp) REVERT: i 19 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8041 (mmt90) REVERT: i 107 ASP cc_start: 0.8097 (p0) cc_final: 0.7828 (p0) REVERT: j 34 PHE cc_start: 0.8672 (t80) cc_final: 0.8448 (t80) REVERT: j 35 TRP cc_start: 0.7682 (t60) cc_final: 0.6238 (t60) REVERT: j 61 ASP cc_start: 0.7160 (m-30) cc_final: 0.6359 (t70) REVERT: k 74 LYS cc_start: 0.8185 (tmtm) cc_final: 0.7976 (ttpp) REVERT: l 70 MET cc_start: 0.8144 (mtt) cc_final: 0.7826 (mtm) REVERT: m 28 THR cc_start: 0.9122 (m) cc_final: 0.8789 (p) REVERT: m 43 LYS cc_start: 0.8733 (tmtp) cc_final: 0.8516 (tptp) REVERT: m 50 TYR cc_start: 0.7931 (t80) cc_final: 0.7690 (t80) REVERT: m 107 ASP cc_start: 0.7486 (t0) cc_final: 0.7088 (t0) REVERT: n 61 GLN cc_start: 0.7458 (mm110) cc_final: 0.6967 (tp-100) REVERT: o 17 ASP cc_start: 0.7630 (p0) cc_final: 0.7383 (p0) REVERT: o 71 ASP cc_start: 0.8173 (p0) cc_final: 0.7425 (p0) REVERT: o 75 ASN cc_start: 0.7691 (p0) cc_final: 0.6721 (t0) REVERT: o 88 TYR cc_start: 0.7767 (t80) cc_final: 0.7559 (t80) REVERT: p 7 ASP cc_start: 0.7351 (m-30) cc_final: 0.5343 (m-30) REVERT: p 31 TYR cc_start: 0.6837 (t80) cc_final: 0.6500 (t80) REVERT: p 42 TRP cc_start: 0.7132 (t-100) cc_final: 0.6805 (t60) REVERT: p 70 VAL cc_start: 0.8603 (p) cc_final: 0.8313 (p) REVERT: p 86 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7566 (mt-10) REVERT: p 106 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7049 (mm-40) REVERT: q 5 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7042 (tm-30) REVERT: q 61 TRP cc_start: 0.9141 (p90) cc_final: 0.8383 (p90) REVERT: r 22 LYS cc_start: 0.6836 (mtpt) cc_final: 0.6428 (mttm) outliers start: 16 outliers final: 3 residues processed: 2513 average time/residue: 0.6811 time to fit residues: 2833.3753 Evaluate side-chains 1419 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1413 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 49 GLU Chi-restraints excluded: chain X residue 53 ARG Chi-restraints excluded: chain i residue 19 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 665 optimal weight: 1.9990 chunk 597 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 402 optimal weight: 1.9990 chunk 319 optimal weight: 1.9990 chunk 617 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 375 optimal weight: 3.9990 chunk 459 optimal weight: 0.9980 chunk 715 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN B 92 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 67 HIS C 128 ASN D 84 HIS ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 347 HIS E 15 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 ASN G 82 ASN ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 GLN G 546 GLN H 124 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 235 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 HIS ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 58 ASN ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 444 ASN L 452 ASN L 572 ASN ** L 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN M 51 ASN M 88 ASN M 92 GLN M 175 ASN M 193 ASN ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 144 GLN N 274 ASN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 30 ASN O 204 ASN O 264 GLN O 294 ASN ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 HIS P 44 GLN P 87 HIS P 89 ASN P 136 ASN ** P 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 216 ASN P 234 ASN P 240 HIS P 250 HIS Q 29 HIS Q 44 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS R 54 HIS ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 GLN W 128 HIS X 103 GLN X 150 ASN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 ASN d 27 ASN d 61 GLN e 44 HIS e 81 GLN ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 12 HIS f 50 ASN g 23 GLN ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 82 HIS j 42 HIS k 65 ASN l 27 ASN l 54 GLN l 65 HIS ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 58 ASN p 90 GLN ** p 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 113 HIS q 116 ASN r 8 GLN r 46 HIS ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.310 66577 Z= 0.598 Angle : 1.727 51.618 90329 Z= 1.082 Chirality : 0.308 6.464 9974 Planarity : 0.006 0.133 11402 Dihedral : 9.269 171.616 8927 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.30 % Allowed : 13.21 % Favored : 86.49 % Rotamer: Outliers : 3.30 % Allowed : 14.74 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.08), residues: 7951 helix: -2.33 (0.07), residues: 3758 sheet: -3.52 (0.23), residues: 359 loop : -3.42 (0.09), residues: 3834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP V 96 HIS 0.018 0.002 HIS L 230 PHE 0.036 0.002 PHE L 54 TYR 0.033 0.002 TYR C 209 ARG 0.009 0.001 ARG G 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1920 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1688 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8850 (mp) cc_final: 0.8385 (mp) REVERT: A 61 THR cc_start: 0.8616 (m) cc_final: 0.8410 (p) REVERT: B 96 MET cc_start: 0.7948 (ttm) cc_final: 0.7465 (ttm) REVERT: C 69 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: C 77 ASP cc_start: 0.7530 (m-30) cc_final: 0.7142 (m-30) REVERT: C 83 VAL cc_start: 0.8798 (t) cc_final: 0.8490 (m) REVERT: C 116 PRO cc_start: 0.8751 (Cg_exo) cc_final: 0.8495 (Cg_endo) REVERT: C 118 ASP cc_start: 0.7474 (p0) cc_final: 0.7235 (p0) REVERT: D 19 MET cc_start: 0.6817 (tpp) cc_final: 0.6411 (tpp) REVERT: D 35 ASP cc_start: 0.6643 (t70) cc_final: 0.5931 (t0) REVERT: D 72 MET cc_start: 0.7424 (tpp) cc_final: 0.7120 (tpp) REVERT: D 112 MET cc_start: 0.8267 (mmt) cc_final: 0.7974 (mmm) REVERT: D 145 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8526 (p) REVERT: D 157 HIS cc_start: 0.8616 (t-90) cc_final: 0.8219 (t70) REVERT: D 164 MET cc_start: 0.7401 (pmm) cc_final: 0.6465 (pmm) REVERT: D 168 PHE cc_start: 0.8665 (m-80) cc_final: 0.8366 (m-10) REVERT: D 182 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8522 (tm-30) REVERT: D 189 MET cc_start: 0.8181 (ttt) cc_final: 0.7933 (ttp) REVERT: D 193 TYR cc_start: 0.8762 (t80) cc_final: 0.8540 (t80) REVERT: D 237 ASN cc_start: 0.8715 (p0) cc_final: 0.8443 (p0) REVERT: D 373 GLU cc_start: 0.7384 (tt0) cc_final: 0.6994 (tt0) REVERT: D 410 MET cc_start: 0.7521 (ptp) cc_final: 0.7101 (mtm) REVERT: E 82 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 120 LEU cc_start: 0.8263 (mt) cc_final: 0.7876 (mt) REVERT: F 26 TYR cc_start: 0.6360 (p90) cc_final: 0.5897 (p90) REVERT: F 50 LEU cc_start: 0.8330 (mt) cc_final: 0.7400 (tp) REVERT: F 107 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8591 (m-30) REVERT: F 113 HIS cc_start: 0.7592 (m170) cc_final: 0.7374 (m170) REVERT: F 226 GLU cc_start: 0.7910 (mp0) cc_final: 0.7606 (mp0) REVERT: F 272 MET cc_start: 0.8346 (tpp) cc_final: 0.8097 (tpp) REVERT: F 376 MET cc_start: 0.7675 (mtp) cc_final: 0.7406 (mtp) REVERT: G 94 MET cc_start: 0.7988 (mmm) cc_final: 0.7358 (mmm) REVERT: G 131 LEU cc_start: 0.8415 (pt) cc_final: 0.7750 (tt) REVERT: G 179 ASN cc_start: 0.6756 (p0) cc_final: 0.6166 (t0) REVERT: G 213 TYR cc_start: 0.7197 (t80) cc_final: 0.6862 (t80) REVERT: G 283 MET cc_start: 0.8017 (mtp) cc_final: 0.7812 (mtp) REVERT: G 324 ASP cc_start: 0.7796 (t0) cc_final: 0.5898 (t0) REVERT: G 358 LEU cc_start: 0.7814 (mt) cc_final: 0.7502 (mm) REVERT: G 414 ASP cc_start: 0.7703 (p0) cc_final: 0.7456 (t70) REVERT: G 473 MET cc_start: 0.7956 (tpp) cc_final: 0.7740 (ttp) REVERT: G 504 ASP cc_start: 0.8529 (m-30) cc_final: 0.8156 (t0) REVERT: G 546 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7344 (pp30) REVERT: G 684 MET cc_start: 0.8075 (mmt) cc_final: 0.7790 (mmt) REVERT: H 31 MET cc_start: 0.8968 (mmm) cc_final: 0.8491 (mmm) REVERT: H 35 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8692 (mtpp) REVERT: H 155 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9008 (tm) REVERT: I 16 MET cc_start: 0.6455 (tmt) cc_final: 0.5722 (tmt) REVERT: I 40 LEU cc_start: 0.8823 (tp) cc_final: 0.8529 (tp) REVERT: I 49 THR cc_start: 0.8936 (p) cc_final: 0.8718 (p) REVERT: I 174 ASP cc_start: 0.7552 (t70) cc_final: 0.7317 (t0) REVERT: J 139 ILE cc_start: 0.9407 (mm) cc_final: 0.9112 (mm) REVERT: J 152 MET cc_start: 0.8571 (tpt) cc_final: 0.8297 (tpt) REVERT: K 27 MET cc_start: 0.8496 (tpt) cc_final: 0.8256 (tpt) REVERT: K 36 MET cc_start: 0.7683 (ttm) cc_final: 0.6955 (ttm) REVERT: K 57 MET cc_start: 0.8605 (mmt) cc_final: 0.8304 (mmt) REVERT: K 97 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7882 (pm20) REVERT: L 197 GLU cc_start: 0.8304 (pt0) cc_final: 0.7925 (pt0) REVERT: L 261 VAL cc_start: 0.8502 (m) cc_final: 0.8284 (p) REVERT: L 352 ASP cc_start: 0.6302 (t70) cc_final: 0.5967 (t0) REVERT: L 400 ASN cc_start: 0.7893 (p0) cc_final: 0.7128 (p0) REVERT: L 587 TYR cc_start: 0.8992 (m-10) cc_final: 0.8371 (m-80) REVERT: M 63 THR cc_start: 0.9085 (p) cc_final: 0.8739 (t) REVERT: M 65 LEU cc_start: 0.8795 (mm) cc_final: 0.8588 (mm) REVERT: M 66 ILE cc_start: 0.9401 (mm) cc_final: 0.9124 (mt) REVERT: M 177 MET cc_start: 0.7842 (ppp) cc_final: 0.7523 (ppp) REVERT: M 216 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8591 (tm) REVERT: M 278 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7922 (tpp80) REVERT: M 313 THR cc_start: 0.8698 (p) cc_final: 0.7900 (p) REVERT: M 329 LEU cc_start: 0.9051 (mm) cc_final: 0.8649 (mm) REVERT: M 413 THR cc_start: 0.8864 (p) cc_final: 0.8651 (m) REVERT: M 436 LEU cc_start: 0.8993 (mt) cc_final: 0.8706 (mt) REVERT: M 442 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8328 (mt) REVERT: N 24 THR cc_start: 0.9020 (m) cc_final: 0.8810 (m) REVERT: N 72 LEU cc_start: 0.8511 (tp) cc_final: 0.8186 (tp) REVERT: N 78 TYR cc_start: 0.8228 (t80) cc_final: 0.8004 (t80) REVERT: N 85 MET cc_start: 0.7980 (tpt) cc_final: 0.7348 (tpt) REVERT: N 104 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7745 (ttm) REVERT: N 240 MET cc_start: 0.7358 (tpp) cc_final: 0.7137 (tpp) REVERT: O 165 PRO cc_start: 0.8461 (Cg_endo) cc_final: 0.8067 (Cg_exo) REVERT: O 236 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7883 (mp0) REVERT: P 57 MET cc_start: 0.8480 (mmt) cc_final: 0.8252 (mmt) REVERT: P 82 ARG cc_start: 0.8423 (tpt-90) cc_final: 0.7685 (tmm160) REVERT: Q 39 VAL cc_start: 0.8825 (t) cc_final: 0.8562 (m) REVERT: Q 45 MET cc_start: 0.7970 (mmm) cc_final: 0.7713 (mmm) REVERT: Q 82 MET cc_start: 0.8943 (tpp) cc_final: 0.8735 (tpp) REVERT: R 51 GLU cc_start: 0.7378 (mp0) cc_final: 0.7130 (mp0) REVERT: R 73 ILE cc_start: 0.8881 (mp) cc_final: 0.8349 (mt) REVERT: S 38 GLN cc_start: 0.7244 (tm-30) cc_final: 0.6861 (pp30) REVERT: S 73 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7091 (mp0) REVERT: S 94 LEU cc_start: 0.7449 (mt) cc_final: 0.7019 (mt) REVERT: U 74 GLN cc_start: 0.8538 (tp40) cc_final: 0.7756 (tm-30) REVERT: V 82 GLN cc_start: 0.7990 (tp40) cc_final: 0.7386 (tp40) REVERT: V 96 TRP cc_start: 0.6076 (m-10) cc_final: 0.5854 (m-10) REVERT: W 87 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8292 (mtmm) REVERT: W 90 MET cc_start: 0.8299 (mmm) cc_final: 0.7628 (mmt) REVERT: W 91 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8277 (mp0) REVERT: X 34 GLN cc_start: 0.9066 (mp10) cc_final: 0.8810 (mp10) REVERT: X 43 MET cc_start: 0.8549 (mmm) cc_final: 0.8068 (mmm) REVERT: X 47 TRP cc_start: 0.7427 (m100) cc_final: 0.6958 (m100) REVERT: Y 2 LYS cc_start: 0.6397 (tptt) cc_final: 0.6127 (pttm) REVERT: Y 125 LYS cc_start: 0.8161 (tptm) cc_final: 0.7536 (tttm) REVERT: Z 78 LYS cc_start: 0.8271 (tptt) cc_final: 0.7840 (tptt) REVERT: Z 102 ASN cc_start: 0.5323 (p0) cc_final: 0.4898 (t0) REVERT: Z 122 GLU cc_start: 0.7689 (tp30) cc_final: 0.7390 (tp30) REVERT: Z 124 TYR cc_start: 0.6977 (p90) cc_final: 0.6683 (p90) REVERT: Z 132 MET cc_start: 0.8577 (tpp) cc_final: 0.7626 (tpp) REVERT: b 15 GLU cc_start: 0.7038 (tt0) cc_final: 0.6688 (tt0) REVERT: d 3 ASN cc_start: 0.8309 (p0) cc_final: 0.8103 (m-40) REVERT: d 17 GLU cc_start: 0.7672 (tt0) cc_final: 0.7430 (tt0) REVERT: d 25 LYS cc_start: 0.7986 (ttmp) cc_final: 0.7709 (tttm) REVERT: d 109 TYR cc_start: 0.7716 (m-80) cc_final: 0.7358 (m-80) REVERT: e 3 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7886 (tm) REVERT: f 26 ASP cc_start: 0.8510 (m-30) cc_final: 0.8271 (m-30) REVERT: f 30 ASP cc_start: 0.7278 (m-30) cc_final: 0.6794 (m-30) REVERT: g 23 GLN cc_start: 0.8201 (tp-100) cc_final: 0.7924 (tm-30) REVERT: g 96 LYS cc_start: 0.8820 (ptmm) cc_final: 0.8549 (pttp) REVERT: g 110 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6399 (m-80) REVERT: h 15 LEU cc_start: 0.8341 (mm) cc_final: 0.7647 (pp) REVERT: h 30 MET cc_start: 0.7605 (mmm) cc_final: 0.7377 (ptm) REVERT: i 74 VAL cc_start: 0.8945 (t) cc_final: 0.8675 (p) REVERT: i 84 TYR cc_start: 0.8504 (t80) cc_final: 0.8288 (t80) REVERT: i 107 ASP cc_start: 0.8003 (p0) cc_final: 0.7742 (p0) REVERT: j 26 GLU cc_start: 0.6894 (tt0) cc_final: 0.6344 (tt0) REVERT: j 40 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: l 136 ASN cc_start: 0.7087 (t0) cc_final: 0.6864 (t0) REVERT: m 43 LYS cc_start: 0.8932 (tmtp) cc_final: 0.8602 (tptp) REVERT: m 84 LYS cc_start: 0.6623 (tptt) cc_final: 0.6307 (tptt) REVERT: m 112 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: n 41 CYS cc_start: 0.8609 (m) cc_final: 0.8396 (m) REVERT: n 114 TYR cc_start: 0.7525 (p90) cc_final: 0.6884 (p90) REVERT: o 43 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7016 (tm-30) REVERT: p 7 ASP cc_start: 0.7270 (m-30) cc_final: 0.6946 (m-30) REVERT: p 31 TYR cc_start: 0.7045 (t80) cc_final: 0.6693 (t80) REVERT: q 5 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7440 (tm-30) REVERT: q 48 TYR cc_start: 0.8855 (m-80) cc_final: 0.8608 (m-10) REVERT: q 53 LYS cc_start: 0.9059 (mppt) cc_final: 0.8650 (mppt) REVERT: q 61 TRP cc_start: 0.9078 (p90) cc_final: 0.8467 (p90) REVERT: q 116 ASN cc_start: 0.8506 (t160) cc_final: 0.8022 (t0) REVERT: r 22 LYS cc_start: 0.6964 (mtpt) cc_final: 0.6542 (mttp) REVERT: r 69 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.4435 (mtp) REVERT: r 112 LEU cc_start: 0.7250 (tt) cc_final: 0.6395 (mt) outliers start: 232 outliers final: 113 residues processed: 1816 average time/residue: 0.5885 time to fit residues: 1818.3418 Evaluate side-chains 1451 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1322 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 546 GLN Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain I residue 4 TYR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain J residue 2 ASN Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 578 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 82 ASN Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 442 ILE Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain O residue 236 GLU Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain S residue 93 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain a residue 38 VAL Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain f residue 51 GLU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 56 VAL Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 97 ARG Chi-restraints excluded: chain p residue 27 ASN Chi-restraints excluded: chain p residue 30 THR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 96 ASP Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain s residue 57 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 397 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 595 optimal weight: 3.9990 chunk 487 optimal weight: 9.9990 chunk 197 optimal weight: 0.8980 chunk 716 optimal weight: 8.9990 chunk 774 optimal weight: 8.9990 chunk 638 optimal weight: 7.9990 chunk 710 optimal weight: 0.0980 chunk 244 optimal weight: 5.9990 chunk 575 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 92 GLN B 104 ASN B 137 HIS B 172 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN E 121 GLN E 214 GLN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 GLN ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN G 491 ASN H 93 HIS ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN I 138 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 366 ASN ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 316 HIS ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN P 184 ASN P 288 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 HIS ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 HIS l 27 ASN l 103 HIS ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.291 66577 Z= 0.566 Angle : 1.681 51.181 90329 Z= 1.063 Chirality : 0.312 6.493 9974 Planarity : 0.006 0.126 11402 Dihedral : 8.643 175.041 8913 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.97 % Favored : 86.78 % Rotamer: Outliers : 3.99 % Allowed : 17.17 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.09), residues: 7951 helix: -1.60 (0.08), residues: 3778 sheet: -3.07 (0.25), residues: 362 loop : -3.16 (0.10), residues: 3811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 487 HIS 0.015 0.001 HIS L 230 PHE 0.028 0.002 PHE Y 60 TYR 0.031 0.002 TYR N 146 ARG 0.014 0.001 ARG i 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1786 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1506 time to evaluate : 5.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LEU cc_start: 0.8818 (mp) cc_final: 0.8468 (mp) REVERT: A 68 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 39 GLN cc_start: 0.8502 (pp30) cc_final: 0.7966 (pp30) REVERT: C 77 ASP cc_start: 0.7631 (m-30) cc_final: 0.7226 (m-30) REVERT: C 83 VAL cc_start: 0.8953 (t) cc_final: 0.8626 (m) REVERT: C 116 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8557 (Cg_endo) REVERT: C 118 ASP cc_start: 0.7621 (p0) cc_final: 0.7408 (p0) REVERT: C 135 TRP cc_start: 0.8576 (t-100) cc_final: 0.8276 (t-100) REVERT: C 199 LEU cc_start: 0.7813 (mt) cc_final: 0.7574 (pp) REVERT: D 35 ASP cc_start: 0.6616 (t70) cc_final: 0.5910 (t0) REVERT: D 65 VAL cc_start: 0.8670 (t) cc_final: 0.8465 (p) REVERT: D 72 MET cc_start: 0.7288 (tpp) cc_final: 0.6975 (tpp) REVERT: D 107 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: D 112 MET cc_start: 0.8314 (mmt) cc_final: 0.8075 (mmm) REVERT: D 145 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8703 (p) REVERT: D 157 HIS cc_start: 0.8629 (t-90) cc_final: 0.8244 (t70) REVERT: D 164 MET cc_start: 0.7389 (pmm) cc_final: 0.6381 (ptp) REVERT: D 168 PHE cc_start: 0.8605 (m-80) cc_final: 0.8232 (m-80) REVERT: D 170 MET cc_start: 0.8793 (mmm) cc_final: 0.8372 (mmp) REVERT: D 182 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 189 MET cc_start: 0.8154 (ttt) cc_final: 0.7822 (ttp) REVERT: D 287 ILE cc_start: 0.8935 (tp) cc_final: 0.8707 (tp) REVERT: D 373 GLU cc_start: 0.7486 (tt0) cc_final: 0.7117 (tt0) REVERT: D 410 MET cc_start: 0.7495 (ptp) cc_final: 0.7292 (mtm) REVERT: E 120 LEU cc_start: 0.8114 (mt) cc_final: 0.7823 (mt) REVERT: F 50 LEU cc_start: 0.8412 (mt) cc_final: 0.7582 (tp) REVERT: G 71 MET cc_start: 0.8344 (tpp) cc_final: 0.8091 (tpp) REVERT: G 94 MET cc_start: 0.8385 (mmm) cc_final: 0.7712 (mmm) REVERT: G 131 LEU cc_start: 0.8481 (pt) cc_final: 0.7879 (tt) REVERT: G 187 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7863 (pt) REVERT: G 283 MET cc_start: 0.8145 (mtp) cc_final: 0.7835 (mtp) REVERT: G 414 ASP cc_start: 0.7687 (p0) cc_final: 0.7483 (t70) REVERT: G 491 ASN cc_start: 0.6223 (OUTLIER) cc_final: 0.5935 (p0) REVERT: G 504 ASP cc_start: 0.8378 (m-30) cc_final: 0.8129 (t0) REVERT: G 684 MET cc_start: 0.8047 (mmt) cc_final: 0.7833 (mmt) REVERT: H 195 ARG cc_start: 0.7874 (tpt90) cc_final: 0.7660 (tpt90) REVERT: H 225 MET cc_start: 0.7392 (ttm) cc_final: 0.6962 (mtt) REVERT: I 16 MET cc_start: 0.6478 (tmt) cc_final: 0.5929 (tmt) REVERT: I 40 LEU cc_start: 0.8732 (tp) cc_final: 0.8498 (tp) REVERT: I 49 THR cc_start: 0.9015 (p) cc_final: 0.8809 (p) REVERT: I 174 ASP cc_start: 0.7565 (t70) cc_final: 0.7272 (t0) REVERT: J 122 ASP cc_start: 0.7500 (m-30) cc_final: 0.7272 (m-30) REVERT: J 139 ILE cc_start: 0.9394 (mm) cc_final: 0.8780 (mm) REVERT: J 151 MET cc_start: 0.8007 (mmm) cc_final: 0.7728 (mmm) REVERT: K 36 MET cc_start: 0.7801 (ttm) cc_final: 0.7141 (ttm) REVERT: K 57 MET cc_start: 0.8771 (mmt) cc_final: 0.8483 (mmt) REVERT: K 92 ASN cc_start: 0.7781 (t160) cc_final: 0.7188 (t0) REVERT: K 95 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8529 (pt) REVERT: K 97 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: L 137 MET cc_start: 0.7813 (ttp) cc_final: 0.7554 (ttp) REVERT: L 197 GLU cc_start: 0.8622 (pt0) cc_final: 0.7917 (pt0) REVERT: L 261 VAL cc_start: 0.8720 (m) cc_final: 0.8439 (p) REVERT: L 352 ASP cc_start: 0.6331 (t70) cc_final: 0.5983 (t0) REVERT: L 397 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7410 (mt-10) REVERT: L 400 ASN cc_start: 0.8181 (p0) cc_final: 0.6921 (t0) REVERT: L 466 PHE cc_start: 0.8199 (t80) cc_final: 0.7896 (t80) REVERT: L 486 LEU cc_start: 0.8239 (mm) cc_final: 0.7908 (mm) REVERT: L 587 TYR cc_start: 0.8928 (m-10) cc_final: 0.8268 (m-10) REVERT: M 63 THR cc_start: 0.9185 (p) cc_final: 0.8860 (t) REVERT: M 66 ILE cc_start: 0.9388 (mm) cc_final: 0.9142 (mt) REVERT: M 177 MET cc_start: 0.7819 (ppp) cc_final: 0.7432 (ppp) REVERT: M 216 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8550 (tm) REVERT: M 278 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6778 (ttp80) REVERT: M 310 MET cc_start: 0.7805 (tpt) cc_final: 0.7194 (tpp) REVERT: M 315 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8288 (tm) REVERT: M 329 LEU cc_start: 0.9029 (mm) cc_final: 0.8593 (mm) REVERT: M 376 MET cc_start: 0.8079 (mtp) cc_final: 0.7709 (mtt) REVERT: M 455 THR cc_start: 0.7334 (p) cc_final: 0.7079 (p) REVERT: N 29 MET cc_start: 0.7680 (mtp) cc_final: 0.7466 (mtm) REVERT: N 57 THR cc_start: 0.9089 (p) cc_final: 0.8857 (t) REVERT: N 104 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7725 (ttm) REVERT: N 240 MET cc_start: 0.7552 (tpp) cc_final: 0.7282 (tpp) REVERT: N 278 MET cc_start: 0.8960 (tpp) cc_final: 0.8683 (tpp) REVERT: N 282 MET cc_start: 0.7572 (mtp) cc_final: 0.7254 (mtm) REVERT: O 209 THR cc_start: 0.8068 (m) cc_final: 0.7718 (p) REVERT: P 44 GLN cc_start: 0.8317 (tp40) cc_final: 0.8081 (tp40) REVERT: P 82 ARG cc_start: 0.8450 (tpt-90) cc_final: 0.7896 (tmm160) REVERT: Q 39 VAL cc_start: 0.8942 (t) cc_final: 0.8665 (m) REVERT: Q 45 MET cc_start: 0.7847 (mmm) cc_final: 0.7573 (mmm) REVERT: Q 82 MET cc_start: 0.8880 (tpp) cc_final: 0.8649 (tpp) REVERT: Q 98 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7574 (ttpt) REVERT: R 51 GLU cc_start: 0.7606 (mp0) cc_final: 0.7369 (mp0) REVERT: R 72 TYR cc_start: 0.8629 (m-80) cc_final: 0.8363 (m-80) REVERT: U 74 GLN cc_start: 0.8641 (tp40) cc_final: 0.7592 (tm-30) REVERT: V 57 MET cc_start: 0.8696 (ptp) cc_final: 0.8441 (ptp) REVERT: V 82 GLN cc_start: 0.7549 (tp40) cc_final: 0.6937 (tp40) REVERT: V 96 TRP cc_start: 0.6224 (m-10) cc_final: 0.5792 (m-10) REVERT: W 90 MET cc_start: 0.8342 (mmm) cc_final: 0.8038 (mmp) REVERT: X 47 TRP cc_start: 0.7415 (m100) cc_final: 0.7066 (m100) REVERT: Y 41 SER cc_start: 0.9062 (p) cc_final: 0.8683 (t) REVERT: Z 78 LYS cc_start: 0.8157 (tptt) cc_final: 0.7746 (tptp) REVERT: Z 88 GLU cc_start: 0.8197 (tp30) cc_final: 0.7365 (tp30) REVERT: Z 102 ASN cc_start: 0.5421 (p0) cc_final: 0.4884 (t0) REVERT: Z 124 TYR cc_start: 0.7114 (p90) cc_final: 0.6590 (p90) REVERT: Z 132 MET cc_start: 0.8468 (tpp) cc_final: 0.7428 (tpp) REVERT: b 46 LYS cc_start: 0.8508 (tttm) cc_final: 0.8148 (tttt) REVERT: b 81 LYS cc_start: 0.8066 (mppt) cc_final: 0.7681 (mppt) REVERT: b 82 ASN cc_start: 0.7372 (t0) cc_final: 0.7160 (t0) REVERT: d 14 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6159 (tm) REVERT: d 36 LEU cc_start: 0.8108 (mt) cc_final: 0.7618 (tt) REVERT: d 44 MET cc_start: 0.8432 (tpt) cc_final: 0.7705 (mmt) REVERT: d 47 MET cc_start: 0.6562 (ttt) cc_final: 0.6291 (ttm) REVERT: d 95 LYS cc_start: 0.8962 (tmmt) cc_final: 0.8450 (ttmt) REVERT: d 109 TYR cc_start: 0.7593 (m-80) cc_final: 0.7088 (m-80) REVERT: e 3 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7974 (tm) REVERT: e 18 MET cc_start: 0.7879 (mmm) cc_final: 0.7549 (mmm) REVERT: e 98 SER cc_start: 0.7786 (m) cc_final: 0.7447 (p) REVERT: f 30 ASP cc_start: 0.7238 (m-30) cc_final: 0.6983 (m-30) REVERT: g 23 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7878 (tm-30) REVERT: g 25 GLN cc_start: 0.7265 (tt0) cc_final: 0.7050 (tt0) REVERT: g 96 LYS cc_start: 0.8888 (ptmm) cc_final: 0.8663 (pttp) REVERT: g 110 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.6235 (m-80) REVERT: g 111 PHE cc_start: 0.8212 (m-80) cc_final: 0.7800 (m-10) REVERT: g 117 GLN cc_start: 0.7513 (tm-30) cc_final: 0.6952 (tm-30) REVERT: h 15 LEU cc_start: 0.8309 (mm) cc_final: 0.7548 (pp) REVERT: i 16 GLU cc_start: 0.8241 (tp30) cc_final: 0.7656 (pm20) REVERT: i 89 MET cc_start: 0.8401 (mmm) cc_final: 0.8179 (mmm) REVERT: j 40 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8040 (m-80) REVERT: j 45 ASP cc_start: 0.7983 (t0) cc_final: 0.7728 (t0) REVERT: m 43 LYS cc_start: 0.8907 (tmtp) cc_final: 0.8689 (tptp) REVERT: m 60 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6658 (pt0) REVERT: m 84 LYS cc_start: 0.6687 (tptt) cc_final: 0.6447 (tmtt) REVERT: m 112 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: n 81 PHE cc_start: 0.9090 (m-10) cc_final: 0.8751 (m-10) REVERT: o 43 GLN cc_start: 0.7262 (tm-30) cc_final: 0.7010 (tm-30) REVERT: p 31 TYR cc_start: 0.7101 (t80) cc_final: 0.6746 (t80) REVERT: p 88 GLU cc_start: 0.8232 (tp30) cc_final: 0.7917 (tp30) REVERT: p 92 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8002 (tpp-160) REVERT: p 150 SER cc_start: 0.8913 (m) cc_final: 0.8566 (t) REVERT: q 53 LYS cc_start: 0.9113 (mppt) cc_final: 0.8799 (mppt) REVERT: q 61 TRP cc_start: 0.9202 (p90) cc_final: 0.8396 (p90) REVERT: q 67 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: q 116 ASN cc_start: 0.8570 (t160) cc_final: 0.8143 (t0) REVERT: r 69 MET cc_start: 0.4715 (OUTLIER) cc_final: 0.4038 (mtp) REVERT: r 112 LEU cc_start: 0.7230 (tt) cc_final: 0.6381 (mt) outliers start: 280 outliers final: 142 residues processed: 1661 average time/residue: 0.6009 time to fit residues: 1723.0773 Evaluate side-chains 1452 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1292 time to evaluate : 5.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 389 CYS Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain G residue 30 CYS Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 525 LEU Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 95 LEU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 153 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 426 ILE Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 361 MET Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 304 MET Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 107 GLU Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain Q residue 98 LYS Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 13 HIS Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 23 ILE Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain h residue 37 ILE Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 59 TRP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain l residue 27 ASN Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 79 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain p residue 9 TYR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 104 ILE Chi-restraints excluded: chain p residue 128 LEU Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain s residue 31 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 708 optimal weight: 0.9980 chunk 538 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 481 optimal weight: 0.9990 chunk 719 optimal weight: 0.9980 chunk 761 optimal weight: 9.9990 chunk 375 optimal weight: 0.9980 chunk 681 optimal weight: 0.4980 chunk 205 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN I 159 ASN ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 184 ASN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN k 53 ASN l 27 ASN n 11 HIS ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 138 GLN ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.283 66577 Z= 0.550 Angle : 1.664 51.115 90329 Z= 1.055 Chirality : 0.312 6.457 9974 Planarity : 0.005 0.120 11402 Dihedral : 8.295 177.985 8913 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.26 % Favored : 87.51 % Rotamer: Outliers : 4.07 % Allowed : 19.04 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.09), residues: 7951 helix: -1.18 (0.08), residues: 3718 sheet: -2.70 (0.26), residues: 364 loop : -3.02 (0.10), residues: 3869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 413 HIS 0.016 0.001 HIS f 9 PHE 0.023 0.001 PHE Y 60 TYR 0.033 0.002 TYR n 114 ARG 0.012 0.000 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1754 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1468 time to evaluate : 5.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8895 (t80) cc_final: 0.8540 (t80) REVERT: A 68 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7683 (tm-30) REVERT: B 44 ASP cc_start: 0.8741 (t0) cc_final: 0.8539 (t0) REVERT: B 131 ASN cc_start: 0.8640 (m-40) cc_final: 0.8307 (m110) REVERT: C 39 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: C 69 ASN cc_start: 0.7931 (OUTLIER) cc_final: 0.7673 (m-40) REVERT: C 77 ASP cc_start: 0.7589 (m-30) cc_final: 0.7149 (m-30) REVERT: C 83 VAL cc_start: 0.8954 (t) cc_final: 0.8635 (m) REVERT: C 95 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8472 (m-40) REVERT: C 116 PRO cc_start: 0.8912 (Cg_exo) cc_final: 0.8681 (Cg_endo) REVERT: D 23 LYS cc_start: 0.7756 (ptpp) cc_final: 0.7016 (tptp) REVERT: D 35 ASP cc_start: 0.6589 (t70) cc_final: 0.5912 (t0) REVERT: D 65 VAL cc_start: 0.8651 (t) cc_final: 0.8403 (p) REVERT: D 157 HIS cc_start: 0.8429 (t-90) cc_final: 0.8067 (t70) REVERT: D 164 MET cc_start: 0.7414 (pmm) cc_final: 0.6402 (ptp) REVERT: D 168 PHE cc_start: 0.8515 (m-80) cc_final: 0.7918 (m-80) REVERT: D 170 MET cc_start: 0.8874 (mmm) cc_final: 0.8549 (mmp) REVERT: D 189 MET cc_start: 0.8005 (ttt) cc_final: 0.7625 (ttp) REVERT: D 237 ASN cc_start: 0.8699 (p0) cc_final: 0.8397 (p0) REVERT: D 260 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8254 (pt) REVERT: D 373 GLU cc_start: 0.7496 (tt0) cc_final: 0.6916 (tt0) REVERT: E 74 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6519 (mp10) REVERT: E 82 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7474 (mm-30) REVERT: E 120 LEU cc_start: 0.8022 (mt) cc_final: 0.7545 (mt) REVERT: E 214 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.6088 (pp30) REVERT: F 50 LEU cc_start: 0.8317 (mt) cc_final: 0.7239 (tp) REVERT: F 326 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8167 (mm110) REVERT: G 54 MET cc_start: 0.8413 (tpt) cc_final: 0.7963 (tpt) REVERT: G 71 MET cc_start: 0.8381 (tpp) cc_final: 0.8131 (tpp) REVERT: G 94 MET cc_start: 0.8432 (mmm) cc_final: 0.7834 (mmm) REVERT: G 131 LEU cc_start: 0.8456 (pt) cc_final: 0.7937 (tt) REVERT: G 259 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.5003 (m-40) REVERT: G 283 MET cc_start: 0.8137 (mtp) cc_final: 0.7841 (mtp) REVERT: G 326 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: G 504 ASP cc_start: 0.8285 (m-30) cc_final: 0.7939 (t70) REVERT: H 32 GLN cc_start: 0.9050 (mt0) cc_final: 0.8554 (mt0) REVERT: H 59 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6438 (mm-30) REVERT: H 143 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7766 (mt-10) REVERT: H 150 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8638 (tm) REVERT: H 179 TRP cc_start: 0.7970 (p-90) cc_final: 0.7058 (p-90) REVERT: I 16 MET cc_start: 0.6514 (tmt) cc_final: 0.5813 (tmt) REVERT: I 22 ASN cc_start: 0.8043 (t0) cc_final: 0.7632 (t0) REVERT: I 28 MET cc_start: 0.8065 (tpt) cc_final: 0.6445 (tpt) REVERT: I 38 MET cc_start: 0.8140 (tmm) cc_final: 0.7622 (tmm) REVERT: I 40 LEU cc_start: 0.8760 (tp) cc_final: 0.8419 (tp) REVERT: I 174 ASP cc_start: 0.7544 (t70) cc_final: 0.7228 (t0) REVERT: J 151 MET cc_start: 0.8049 (mmm) cc_final: 0.7769 (mmm) REVERT: K 92 ASN cc_start: 0.7852 (t160) cc_final: 0.7138 (t0) REVERT: K 97 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: L 59 MET cc_start: 0.7232 (mmm) cc_final: 0.7012 (mmm) REVERT: L 101 MET cc_start: 0.9246 (mmp) cc_final: 0.9035 (mmp) REVERT: L 197 GLU cc_start: 0.8608 (pt0) cc_final: 0.8230 (pt0) REVERT: L 226 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6535 (mm-40) REVERT: L 261 VAL cc_start: 0.8731 (m) cc_final: 0.8475 (p) REVERT: L 352 ASP cc_start: 0.6589 (t70) cc_final: 0.6281 (t0) REVERT: L 400 ASN cc_start: 0.7900 (p0) cc_final: 0.6952 (t0) REVERT: L 486 LEU cc_start: 0.8061 (mm) cc_final: 0.7667 (mt) REVERT: L 550 LEU cc_start: 0.9077 (tt) cc_final: 0.8869 (tp) REVERT: L 587 TYR cc_start: 0.8884 (m-10) cc_final: 0.8228 (m-10) REVERT: M 47 GLU cc_start: 0.8273 (pm20) cc_final: 0.7561 (pm20) REVERT: M 63 THR cc_start: 0.9145 (p) cc_final: 0.8797 (t) REVERT: M 66 ILE cc_start: 0.9311 (mm) cc_final: 0.9086 (mt) REVERT: M 77 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9026 (tm) REVERT: M 177 MET cc_start: 0.7829 (ppp) cc_final: 0.7429 (ppp) REVERT: M 216 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8564 (tm) REVERT: M 276 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7535 (t) REVERT: M 315 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8397 (tm) REVERT: M 350 MET cc_start: 0.8572 (ptp) cc_final: 0.8335 (ptp) REVERT: M 376 MET cc_start: 0.8013 (mtp) cc_final: 0.7715 (ttt) REVERT: M 413 THR cc_start: 0.8999 (p) cc_final: 0.8797 (m) REVERT: N 29 MET cc_start: 0.7745 (mtp) cc_final: 0.7498 (mtm) REVERT: N 79 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8229 (tppt) REVERT: N 104 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7702 (ttm) REVERT: N 190 MET cc_start: 0.7924 (mtm) cc_final: 0.7663 (ptp) REVERT: N 240 MET cc_start: 0.7566 (tpp) cc_final: 0.7325 (tpp) REVERT: N 282 MET cc_start: 0.7533 (mtp) cc_final: 0.7095 (mtm) REVERT: N 337 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9091 (tm) REVERT: O 132 PHE cc_start: 0.8466 (p90) cc_final: 0.8199 (p90) REVERT: O 209 THR cc_start: 0.8030 (m) cc_final: 0.7682 (p) REVERT: P 57 MET cc_start: 0.8541 (tpp) cc_final: 0.8188 (mmt) REVERT: P 82 ARG cc_start: 0.8449 (tpt-90) cc_final: 0.7879 (tmm160) REVERT: Q 39 VAL cc_start: 0.8968 (t) cc_final: 0.8656 (m) REVERT: Q 45 MET cc_start: 0.7798 (mmm) cc_final: 0.7518 (mmm) REVERT: R 72 TYR cc_start: 0.8618 (m-80) cc_final: 0.8239 (m-80) REVERT: T 21 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (pp) REVERT: U 74 GLN cc_start: 0.8739 (tp40) cc_final: 0.7754 (tm-30) REVERT: V 57 MET cc_start: 0.8713 (ptp) cc_final: 0.8437 (ptp) REVERT: V 96 TRP cc_start: 0.6474 (m-10) cc_final: 0.5989 (m-10) REVERT: W 90 MET cc_start: 0.8335 (mmm) cc_final: 0.8067 (mmp) REVERT: Y 41 SER cc_start: 0.9045 (p) cc_final: 0.8659 (t) REVERT: Z 32 TYR cc_start: 0.6006 (m-10) cc_final: 0.5489 (m-10) REVERT: Z 60 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8581 (tt) REVERT: Z 78 LYS cc_start: 0.8099 (tptt) cc_final: 0.7692 (tptp) REVERT: Z 102 ASN cc_start: 0.5283 (p0) cc_final: 0.4758 (t0) REVERT: Z 124 TYR cc_start: 0.7094 (p90) cc_final: 0.6640 (p90) REVERT: Z 132 MET cc_start: 0.8449 (tpp) cc_final: 0.7332 (tpp) REVERT: b 46 LYS cc_start: 0.8522 (tttm) cc_final: 0.8099 (tttt) REVERT: b 82 ASN cc_start: 0.7326 (t0) cc_final: 0.6970 (t0) REVERT: d 14 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6011 (tm) REVERT: d 43 LEU cc_start: 0.8934 (tp) cc_final: 0.8620 (tp) REVERT: d 44 MET cc_start: 0.8441 (tpt) cc_final: 0.7668 (mmt) REVERT: d 47 MET cc_start: 0.6626 (ttt) cc_final: 0.6314 (ttm) REVERT: d 58 LEU cc_start: 0.7629 (mm) cc_final: 0.7397 (mm) REVERT: d 95 LYS cc_start: 0.9076 (tmmt) cc_final: 0.8497 (ttmt) REVERT: d 111 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: e 3 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7993 (tm) REVERT: e 98 SER cc_start: 0.7724 (m) cc_final: 0.7427 (p) REVERT: f 30 ASP cc_start: 0.7324 (m-30) cc_final: 0.7022 (m-30) REVERT: f 48 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5157 (ptm-80) REVERT: g 23 GLN cc_start: 0.8098 (tp-100) cc_final: 0.7863 (tm-30) REVERT: g 25 GLN cc_start: 0.7048 (tt0) cc_final: 0.6738 (tt0) REVERT: g 85 GLU cc_start: 0.8066 (tt0) cc_final: 0.7748 (tt0) REVERT: g 110 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: g 117 GLN cc_start: 0.7501 (tm-30) cc_final: 0.6982 (tm-30) REVERT: h 15 LEU cc_start: 0.8280 (mm) cc_final: 0.7952 (mt) REVERT: h 114 MET cc_start: 0.7650 (mtt) cc_final: 0.7302 (mtt) REVERT: i 116 ILE cc_start: 0.8014 (pt) cc_final: 0.7764 (pt) REVERT: j 40 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: j 45 ASP cc_start: 0.7860 (t0) cc_final: 0.7589 (t0) REVERT: l 74 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8230 (tm-30) REVERT: m 49 GLN cc_start: 0.9016 (tt0) cc_final: 0.8685 (mt0) REVERT: m 60 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6628 (pt0) REVERT: m 84 LYS cc_start: 0.6813 (tptt) cc_final: 0.6562 (tmtt) REVERT: m 112 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: n 100 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7398 (tm-30) REVERT: n 141 GLU cc_start: 0.8503 (pp20) cc_final: 0.8238 (pp20) REVERT: o 96 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8395 (mmtp) REVERT: p 16 THR cc_start: 0.7658 (p) cc_final: 0.7387 (p) REVERT: p 31 TYR cc_start: 0.7081 (t80) cc_final: 0.6666 (t80) REVERT: p 88 GLU cc_start: 0.7974 (tp30) cc_final: 0.7748 (tp30) REVERT: p 92 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7937 (tpp-160) REVERT: p 150 SER cc_start: 0.8971 (m) cc_final: 0.8706 (t) REVERT: q 53 LYS cc_start: 0.9051 (mppt) cc_final: 0.8733 (mppt) REVERT: q 61 TRP cc_start: 0.9143 (p90) cc_final: 0.8310 (p90) REVERT: q 67 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: q 116 ASN cc_start: 0.8525 (t160) cc_final: 0.8063 (t0) REVERT: q 122 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7268 (tm-30) REVERT: r 69 MET cc_start: 0.4489 (OUTLIER) cc_final: 0.4087 (mtp) REVERT: r 111 TYR cc_start: 0.8290 (m-10) cc_final: 0.8074 (m-10) REVERT: r 112 LEU cc_start: 0.7372 (tt) cc_final: 0.6649 (mt) outliers start: 286 outliers final: 144 residues processed: 1633 average time/residue: 0.5961 time to fit residues: 1683.4934 Evaluate side-chains 1451 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1279 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 196 TRP Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 78 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 241 LEU Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 65 CYS Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain Y residue 23 ILE Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 48 ARG Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 6 ASP Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 40 PHE Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 59 TRP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain p residue 9 TYR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 104 ILE Chi-restraints excluded: chain p residue 128 LEU Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain s residue 31 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 634 optimal weight: 0.3980 chunk 432 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 567 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 649 optimal weight: 4.9990 chunk 526 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 chunk 683 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN G 546 GLN G 581 GLN G 629 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN L 29 HIS ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 ASN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 184 ASN P 203 GLN Q 44 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 HIS S 61 GLN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 ASN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 HIS ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 106 GLN p 130 GLN ** p 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.282 66577 Z= 0.559 Angle : 1.664 51.103 90329 Z= 1.056 Chirality : 0.312 6.438 9974 Planarity : 0.005 0.121 11402 Dihedral : 8.060 179.279 8913 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.43 % Favored : 87.35 % Rotamer: Outliers : 4.46 % Allowed : 20.42 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.09), residues: 7951 helix: -0.97 (0.08), residues: 3759 sheet: -2.52 (0.26), residues: 374 loop : -2.97 (0.10), residues: 3818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP L 407 HIS 0.018 0.001 HIS n 11 PHE 0.028 0.002 PHE Y 60 TYR 0.043 0.002 TYR B 135 ARG 0.018 0.000 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1695 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1382 time to evaluate : 5.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 ASN cc_start: 0.8613 (m-40) cc_final: 0.8322 (m110) REVERT: C 39 GLN cc_start: 0.8832 (pp30) cc_final: 0.8355 (pp30) REVERT: C 69 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: C 77 ASP cc_start: 0.7621 (m-30) cc_final: 0.7223 (m-30) REVERT: C 83 VAL cc_start: 0.9017 (t) cc_final: 0.8661 (m) REVERT: C 94 TYR cc_start: 0.9110 (m-80) cc_final: 0.8881 (m-80) REVERT: C 95 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8470 (m-40) REVERT: C 110 TYR cc_start: 0.8310 (p90) cc_final: 0.8084 (p90) REVERT: C 116 PRO cc_start: 0.9152 (Cg_exo) cc_final: 0.8915 (Cg_endo) REVERT: D 23 LYS cc_start: 0.7788 (ptpp) cc_final: 0.7037 (tptp) REVERT: D 35 ASP cc_start: 0.6857 (t70) cc_final: 0.6101 (t0) REVERT: D 72 MET cc_start: 0.7188 (tpp) cc_final: 0.6685 (tpp) REVERT: D 157 HIS cc_start: 0.8412 (t-90) cc_final: 0.8089 (t70) REVERT: D 164 MET cc_start: 0.7559 (pmm) cc_final: 0.6773 (ptp) REVERT: D 168 PHE cc_start: 0.8650 (m-80) cc_final: 0.7969 (m-80) REVERT: D 170 MET cc_start: 0.8948 (mmm) cc_final: 0.8551 (mmp) REVERT: D 189 MET cc_start: 0.8164 (ttt) cc_final: 0.7880 (ttp) REVERT: D 233 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7181 (mtt180) REVERT: D 237 ASN cc_start: 0.8805 (p0) cc_final: 0.8559 (p0) REVERT: D 367 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7666 (tp) REVERT: D 373 GLU cc_start: 0.7508 (tt0) cc_final: 0.6892 (tt0) REVERT: D 410 MET cc_start: 0.7413 (mtm) cc_final: 0.7169 (mtm) REVERT: E 74 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6564 (mp10) REVERT: E 82 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7429 (mm-30) REVERT: E 120 LEU cc_start: 0.7929 (mt) cc_final: 0.7696 (mt) REVERT: F 50 LEU cc_start: 0.8232 (mt) cc_final: 0.7217 (tp) REVERT: F 326 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8179 (mm110) REVERT: F 388 GLU cc_start: 0.7657 (mp0) cc_final: 0.7289 (mp0) REVERT: G 54 MET cc_start: 0.8427 (tpt) cc_final: 0.8026 (tpt) REVERT: G 94 MET cc_start: 0.8599 (mmm) cc_final: 0.8185 (mmm) REVERT: G 107 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8302 (mm) REVERT: G 131 LEU cc_start: 0.8518 (pt) cc_final: 0.7954 (tt) REVERT: G 187 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7855 (pp) REVERT: G 504 ASP cc_start: 0.8298 (m-30) cc_final: 0.7926 (t70) REVERT: H 32 GLN cc_start: 0.9106 (mt0) cc_final: 0.8527 (mt0) REVERT: H 59 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6497 (mm-30) REVERT: H 143 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8007 (mt-10) REVERT: H 179 TRP cc_start: 0.7877 (p-90) cc_final: 0.6942 (p-90) REVERT: H 281 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7964 (tmm-80) REVERT: H 284 GLN cc_start: 0.8473 (mt0) cc_final: 0.7724 (mt0) REVERT: I 16 MET cc_start: 0.6533 (tmt) cc_final: 0.5799 (tmt) REVERT: I 22 ASN cc_start: 0.8017 (t0) cc_final: 0.7585 (t0) REVERT: I 28 MET cc_start: 0.8048 (tpt) cc_final: 0.6402 (tpt) REVERT: I 38 MET cc_start: 0.8109 (tmm) cc_final: 0.7813 (tmm) REVERT: I 174 ASP cc_start: 0.7623 (t70) cc_final: 0.7153 (t0) REVERT: J 11 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8718 (tt) REVERT: K 21 MET cc_start: 0.7600 (mmm) cc_final: 0.6906 (ptp) REVERT: K 23 ARG cc_start: 0.6494 (mtp-110) cc_final: 0.5572 (mmt180) REVERT: K 27 MET cc_start: 0.8484 (mmm) cc_final: 0.8116 (tpp) REVERT: K 92 ASN cc_start: 0.7898 (t160) cc_final: 0.7454 (t0) REVERT: K 97 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8018 (pm20) REVERT: L 101 MET cc_start: 0.9233 (mmp) cc_final: 0.9017 (mmp) REVERT: L 150 MET cc_start: 0.8145 (ttm) cc_final: 0.7878 (ttp) REVERT: L 197 GLU cc_start: 0.8642 (pt0) cc_final: 0.8241 (pt0) REVERT: L 261 VAL cc_start: 0.8757 (m) cc_final: 0.8485 (p) REVERT: L 319 MET cc_start: 0.7818 (mpp) cc_final: 0.7273 (mpp) REVERT: L 352 ASP cc_start: 0.6716 (t70) cc_final: 0.6405 (t0) REVERT: L 383 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7559 (mmp) REVERT: L 397 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7210 (mt-10) REVERT: L 400 ASN cc_start: 0.7895 (p0) cc_final: 0.7076 (t0) REVERT: L 486 LEU cc_start: 0.8266 (mm) cc_final: 0.7983 (mt) REVERT: L 503 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7580 (mm-30) REVERT: L 587 TYR cc_start: 0.8870 (m-10) cc_final: 0.8224 (m-10) REVERT: M 63 THR cc_start: 0.9206 (p) cc_final: 0.8933 (t) REVERT: M 66 ILE cc_start: 0.9366 (mm) cc_final: 0.9106 (mt) REVERT: M 216 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8581 (tm) REVERT: M 276 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7589 (t) REVERT: M 286 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7963 (mp) REVERT: M 315 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8422 (tm) REVERT: M 376 MET cc_start: 0.8247 (mtp) cc_final: 0.7948 (ttt) REVERT: N 79 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8365 (tppt) REVERT: N 104 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7867 (ttm) REVERT: N 240 MET cc_start: 0.7775 (tpp) cc_final: 0.7379 (tpp) REVERT: N 243 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8302 (tpp) REVERT: N 282 MET cc_start: 0.7592 (mtp) cc_final: 0.7210 (mtm) REVERT: N 337 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9149 (tm) REVERT: O 131 ASP cc_start: 0.8033 (t70) cc_final: 0.7446 (t70) REVERT: O 132 PHE cc_start: 0.8503 (p90) cc_final: 0.8280 (p90) REVERT: O 209 THR cc_start: 0.8038 (m) cc_final: 0.7707 (p) REVERT: P 57 MET cc_start: 0.8638 (tpp) cc_final: 0.8294 (mmt) REVERT: P 82 ARG cc_start: 0.8461 (tpt-90) cc_final: 0.7872 (tmm160) REVERT: Q 39 VAL cc_start: 0.8980 (t) cc_final: 0.8642 (m) REVERT: Q 45 MET cc_start: 0.7869 (mmm) cc_final: 0.7621 (mmm) REVERT: R 57 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7255 (tp) REVERT: R 72 TYR cc_start: 0.8599 (m-80) cc_final: 0.8225 (m-80) REVERT: S 39 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7453 (ttp-170) REVERT: T 21 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7461 (pp) REVERT: T 76 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8109 (mm) REVERT: U 74 GLN cc_start: 0.8715 (tp40) cc_final: 0.8268 (tp40) REVERT: V 57 MET cc_start: 0.8735 (ptp) cc_final: 0.8358 (ptp) REVERT: V 86 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: V 96 TRP cc_start: 0.6142 (m-10) cc_final: 0.5775 (m-10) REVERT: W 44 GLU cc_start: 0.8457 (tt0) cc_final: 0.7999 (tt0) REVERT: W 90 MET cc_start: 0.8315 (mmm) cc_final: 0.7914 (mmp) REVERT: W 96 ILE cc_start: 0.8617 (tt) cc_final: 0.8412 (tp) REVERT: X 43 MET cc_start: 0.8730 (mmm) cc_final: 0.7388 (mmm) REVERT: X 47 TRP cc_start: 0.7724 (m100) cc_final: 0.7443 (m100) REVERT: Y 41 SER cc_start: 0.9066 (p) cc_final: 0.8737 (t) REVERT: Y 116 TYR cc_start: 0.8582 (m-10) cc_final: 0.8251 (m-80) REVERT: Z 32 TYR cc_start: 0.6071 (m-10) cc_final: 0.5551 (m-10) REVERT: Z 60 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8607 (tt) REVERT: Z 78 LYS cc_start: 0.8082 (tptt) cc_final: 0.7819 (tptt) REVERT: Z 124 TYR cc_start: 0.6949 (p90) cc_final: 0.6463 (p90) REVERT: Z 132 MET cc_start: 0.8357 (tpp) cc_final: 0.7406 (tpp) REVERT: b 15 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7686 (mt-10) REVERT: b 43 MET cc_start: 0.8210 (mtp) cc_final: 0.7970 (mtm) REVERT: b 46 LYS cc_start: 0.8512 (tttm) cc_final: 0.8099 (tttt) REVERT: b 82 ASN cc_start: 0.7342 (t0) cc_final: 0.6996 (t0) REVERT: d 14 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6272 (tm) REVERT: d 36 LEU cc_start: 0.8161 (mt) cc_final: 0.7582 (tt) REVERT: d 43 LEU cc_start: 0.8946 (tp) cc_final: 0.8612 (tp) REVERT: d 47 MET cc_start: 0.6615 (ttt) cc_final: 0.6303 (ttm) REVERT: d 95 LYS cc_start: 0.9098 (tmmt) cc_final: 0.8505 (ttmt) REVERT: d 111 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: e 3 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8142 (tp) REVERT: e 18 MET cc_start: 0.7975 (mmm) cc_final: 0.7452 (mmm) REVERT: e 77 ASP cc_start: 0.7431 (m-30) cc_final: 0.7201 (m-30) REVERT: e 98 SER cc_start: 0.7990 (m) cc_final: 0.7620 (p) REVERT: f 30 ASP cc_start: 0.7367 (m-30) cc_final: 0.6808 (m-30) REVERT: g 23 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7920 (tm-30) REVERT: g 25 GLN cc_start: 0.7035 (tt0) cc_final: 0.6753 (tt0) REVERT: g 85 GLU cc_start: 0.8007 (tt0) cc_final: 0.7736 (tt0) REVERT: g 117 GLN cc_start: 0.7551 (tm-30) cc_final: 0.6912 (tm-30) REVERT: h 114 MET cc_start: 0.7784 (mtt) cc_final: 0.7478 (mtt) REVERT: i 107 ASP cc_start: 0.7886 (p0) cc_final: 0.7370 (p0) REVERT: j 43 ASP cc_start: 0.7724 (t0) cc_final: 0.7369 (t0) REVERT: j 45 ASP cc_start: 0.7861 (t0) cc_final: 0.7528 (t0) REVERT: l 74 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8112 (tm-30) REVERT: m 49 GLN cc_start: 0.9029 (tt0) cc_final: 0.8555 (mt0) REVERT: m 60 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6606 (pt0) REVERT: m 84 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6230 (tttt) REVERT: m 112 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: n 11 HIS cc_start: 0.7092 (OUTLIER) cc_final: 0.6797 (t70) REVERT: n 100 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7644 (tm-30) REVERT: n 149 MET cc_start: 0.6769 (mtm) cc_final: 0.6538 (mtm) REVERT: o 96 LYS cc_start: 0.8552 (mmtp) cc_final: 0.7967 (mtmt) REVERT: p 31 TYR cc_start: 0.7151 (t80) cc_final: 0.6708 (t80) REVERT: q 53 LYS cc_start: 0.9166 (mppt) cc_final: 0.8754 (mppt) REVERT: q 61 TRP cc_start: 0.9159 (p90) cc_final: 0.8426 (p90) REVERT: q 67 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: q 122 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7551 (tm-30) REVERT: r 22 LYS cc_start: 0.7021 (ttmt) cc_final: 0.6820 (tttt) REVERT: r 69 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.4295 (mtp) REVERT: r 112 LEU cc_start: 0.7381 (tt) cc_final: 0.6703 (mt) outliers start: 313 outliers final: 192 residues processed: 1574 average time/residue: 0.5706 time to fit residues: 1556.0173 Evaluate side-chains 1498 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1275 time to evaluate : 5.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 214 GLN Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 546 GLN Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 479 VAL Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 286 ILE Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 314 MET Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 360 LEU Chi-restraints excluded: chain M residue 361 MET Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain N residue 337 LEU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 93 MET Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Y residue 23 ILE Chi-restraints excluded: chain Y residue 33 ILE Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Z residue 49 MET Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 34 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 18 ASP Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain h residue 140 THR Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 113 PHE Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 90 GLU Chi-restraints excluded: chain p residue 9 TYR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 104 ILE Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain s residue 31 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 256 optimal weight: 6.9990 chunk 685 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 447 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 762 optimal weight: 10.0000 chunk 632 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 400 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 581 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 220 HIS N 80 GLN ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 67 GLN P 131 HIS ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 HIS P 184 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 30 GLN ** S 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN ** l 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 154 HIS ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 17 HIS ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 135 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.281 66577 Z= 0.585 Angle : 1.678 51.100 90329 Z= 1.062 Chirality : 0.312 6.436 9974 Planarity : 0.005 0.104 11402 Dihedral : 7.927 178.347 8913 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.82 % Favored : 86.98 % Rotamer: Outliers : 5.14 % Allowed : 20.98 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.09), residues: 7951 helix: -0.84 (0.08), residues: 3748 sheet: -2.55 (0.26), residues: 385 loop : -2.90 (0.10), residues: 3818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 487 HIS 0.030 0.002 HIS n 11 PHE 0.030 0.002 PHE Y 60 TYR 0.043 0.002 TYR B 135 ARG 0.014 0.001 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1725 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1364 time to evaluate : 5.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.9108 (tp) cc_final: 0.8895 (tp) REVERT: B 126 MET cc_start: 0.8127 (ttm) cc_final: 0.7567 (ttt) REVERT: C 39 GLN cc_start: 0.8835 (pp30) cc_final: 0.8567 (pp30) REVERT: C 77 ASP cc_start: 0.7629 (m-30) cc_final: 0.7291 (m-30) REVERT: D 23 LYS cc_start: 0.7794 (ptpp) cc_final: 0.7124 (tptp) REVERT: D 35 ASP cc_start: 0.7088 (t70) cc_final: 0.6352 (t0) REVERT: D 72 MET cc_start: 0.7480 (tpp) cc_final: 0.7123 (tpp) REVERT: D 107 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: D 157 HIS cc_start: 0.8330 (t-90) cc_final: 0.8120 (t70) REVERT: D 189 MET cc_start: 0.8149 (ttt) cc_final: 0.7884 (ttp) REVERT: D 233 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7451 (mtt180) REVERT: D 342 MET cc_start: 0.8814 (mmm) cc_final: 0.8484 (tpp) REVERT: D 373 GLU cc_start: 0.7285 (tt0) cc_final: 0.6844 (tt0) REVERT: D 410 MET cc_start: 0.7503 (mtm) cc_final: 0.7250 (mtm) REVERT: E 74 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: E 82 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7509 (mm-30) REVERT: E 101 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8440 (mt0) REVERT: E 104 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8506 (m) REVERT: E 121 GLN cc_start: 0.7829 (mt0) cc_final: 0.7579 (mt0) REVERT: F 50 LEU cc_start: 0.8295 (mt) cc_final: 0.7396 (tp) REVERT: F 272 MET cc_start: 0.9102 (tpt) cc_final: 0.8783 (mmm) REVERT: F 326 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8189 (mm110) REVERT: F 388 GLU cc_start: 0.7664 (mp0) cc_final: 0.7310 (mp0) REVERT: G 54 MET cc_start: 0.8566 (tpt) cc_final: 0.8181 (tpt) REVERT: G 94 MET cc_start: 0.8725 (mmm) cc_final: 0.8296 (mmm) REVERT: G 107 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8316 (mm) REVERT: G 131 LEU cc_start: 0.8738 (pt) cc_final: 0.8019 (tt) REVERT: G 187 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8096 (pt) REVERT: G 504 ASP cc_start: 0.8397 (m-30) cc_final: 0.7955 (t70) REVERT: G 512 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: H 59 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6474 (mm-30) REVERT: H 143 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8091 (mt-10) REVERT: H 155 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9107 (tm) REVERT: H 179 TRP cc_start: 0.7855 (p-90) cc_final: 0.6874 (p-90) REVERT: H 195 ARG cc_start: 0.7811 (tpt90) cc_final: 0.6910 (tpt90) REVERT: I 16 MET cc_start: 0.6486 (tmt) cc_final: 0.5970 (tmt) REVERT: I 22 ASN cc_start: 0.8013 (t0) cc_final: 0.7522 (t0) REVERT: I 28 MET cc_start: 0.7989 (tpt) cc_final: 0.6372 (tpt) REVERT: I 38 MET cc_start: 0.8186 (tmm) cc_final: 0.7881 (tmm) REVERT: I 96 ILE cc_start: 0.7844 (mp) cc_final: 0.7633 (mp) REVERT: I 166 GLU cc_start: 0.8305 (tt0) cc_final: 0.8070 (tt0) REVERT: I 174 ASP cc_start: 0.7813 (t70) cc_final: 0.7330 (t0) REVERT: J 4 TYR cc_start: 0.8312 (t80) cc_final: 0.8011 (t80) REVERT: J 11 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8833 (tt) REVERT: K 23 ARG cc_start: 0.6548 (mtp-110) cc_final: 0.5259 (mmt180) REVERT: K 27 MET cc_start: 0.8584 (mmm) cc_final: 0.8369 (tpp) REVERT: K 62 THR cc_start: 0.9170 (m) cc_final: 0.8946 (m) REVERT: K 92 ASN cc_start: 0.8055 (t160) cc_final: 0.7622 (t0) REVERT: K 97 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8122 (pm20) REVERT: L 60 GLU cc_start: 0.7694 (mp0) cc_final: 0.7442 (mp0) REVERT: L 150 MET cc_start: 0.8134 (ttm) cc_final: 0.7710 (ttm) REVERT: L 197 GLU cc_start: 0.8760 (pt0) cc_final: 0.7756 (pt0) REVERT: L 201 ILE cc_start: 0.8917 (mt) cc_final: 0.8464 (mt) REVERT: L 251 THR cc_start: 0.9059 (p) cc_final: 0.8848 (p) REVERT: L 261 VAL cc_start: 0.8876 (m) cc_final: 0.8601 (p) REVERT: L 352 ASP cc_start: 0.6752 (t70) cc_final: 0.6441 (t0) REVERT: L 383 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7595 (mmp) REVERT: L 400 ASN cc_start: 0.7853 (p0) cc_final: 0.6927 (t0) REVERT: L 503 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7651 (mm-30) REVERT: L 550 LEU cc_start: 0.8785 (tp) cc_final: 0.8492 (tp) REVERT: L 587 TYR cc_start: 0.8861 (m-10) cc_final: 0.8185 (m-10) REVERT: M 63 THR cc_start: 0.9256 (p) cc_final: 0.8988 (t) REVERT: M 66 ILE cc_start: 0.9490 (mm) cc_final: 0.9237 (mt) REVERT: M 196 TRP cc_start: 0.8195 (t60) cc_final: 0.7803 (t60) REVERT: M 216 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8582 (tm) REVERT: M 257 MET cc_start: 0.6865 (tpp) cc_final: 0.6099 (tpp) REVERT: M 276 CYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7712 (t) REVERT: M 278 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6828 (ttp80) REVERT: M 286 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7995 (mp) REVERT: M 315 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8513 (tm) REVERT: M 376 MET cc_start: 0.8407 (mtp) cc_final: 0.8038 (ttt) REVERT: N 79 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8587 (tppt) REVERT: N 148 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8185 (pp) REVERT: N 220 MET cc_start: 0.8878 (mmt) cc_final: 0.8609 (mmt) REVERT: N 243 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8315 (tpp) REVERT: N 282 MET cc_start: 0.7827 (mtp) cc_final: 0.7454 (mtm) REVERT: O 131 ASP cc_start: 0.8213 (t70) cc_final: 0.7598 (t70) REVERT: O 132 PHE cc_start: 0.8712 (p90) cc_final: 0.8457 (p90) REVERT: O 214 MET cc_start: 0.8022 (tpp) cc_final: 0.7698 (tpp) REVERT: O 271 ASN cc_start: 0.7887 (m-40) cc_final: 0.7564 (t0) REVERT: P 57 MET cc_start: 0.8688 (tpp) cc_final: 0.8330 (mmt) REVERT: P 82 ARG cc_start: 0.8486 (tpt-90) cc_final: 0.7842 (tmm160) REVERT: Q 39 VAL cc_start: 0.9015 (t) cc_final: 0.8716 (m) REVERT: R 57 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7414 (tp) REVERT: R 72 TYR cc_start: 0.8671 (m-80) cc_final: 0.8315 (m-80) REVERT: S 39 ARG cc_start: 0.7750 (ttp-170) cc_final: 0.7328 (ttp-170) REVERT: T 21 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7563 (pp) REVERT: T 76 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8131 (mm) REVERT: U 74 GLN cc_start: 0.8659 (tp40) cc_final: 0.8271 (tp40) REVERT: V 57 MET cc_start: 0.8694 (ptp) cc_final: 0.8322 (ptp) REVERT: V 81 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8157 (tm) REVERT: V 95 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8177 (pttt) REVERT: V 96 TRP cc_start: 0.6673 (m-10) cc_final: 0.6057 (m-10) REVERT: W 44 GLU cc_start: 0.8355 (tt0) cc_final: 0.7945 (tt0) REVERT: W 90 MET cc_start: 0.8346 (mmm) cc_final: 0.7870 (mmp) REVERT: X 47 TRP cc_start: 0.7745 (m100) cc_final: 0.7313 (m100) REVERT: Y 41 SER cc_start: 0.9070 (p) cc_final: 0.8802 (t) REVERT: Z 32 TYR cc_start: 0.6320 (m-10) cc_final: 0.5607 (m-10) REVERT: Z 60 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (tt) REVERT: Z 124 TYR cc_start: 0.6888 (p90) cc_final: 0.6505 (p90) REVERT: Z 132 MET cc_start: 0.8162 (tpp) cc_final: 0.7147 (tpp) REVERT: a 1 MET cc_start: 0.7141 (mmm) cc_final: 0.6615 (mmm) REVERT: b 33 MET cc_start: 0.7111 (mtp) cc_final: 0.6902 (mtp) REVERT: b 46 LYS cc_start: 0.8600 (tttm) cc_final: 0.8180 (tttt) REVERT: b 62 MET cc_start: 0.7011 (ptp) cc_final: 0.6492 (pmm) REVERT: b 82 ASN cc_start: 0.7494 (t0) cc_final: 0.7122 (t0) REVERT: d 14 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6655 (tp) REVERT: d 36 LEU cc_start: 0.8231 (mt) cc_final: 0.7561 (tt) REVERT: d 43 LEU cc_start: 0.8944 (tp) cc_final: 0.8533 (tp) REVERT: d 95 LYS cc_start: 0.9157 (tmmt) cc_final: 0.8939 (tppt) REVERT: d 111 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: e 3 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7905 (tm) REVERT: e 18 MET cc_start: 0.8218 (mmm) cc_final: 0.7706 (mmm) REVERT: e 77 ASP cc_start: 0.7615 (m-30) cc_final: 0.7339 (m-30) REVERT: e 98 SER cc_start: 0.8212 (m) cc_final: 0.7745 (p) REVERT: f 30 ASP cc_start: 0.7369 (m-30) cc_final: 0.6983 (m-30) REVERT: g 23 GLN cc_start: 0.7867 (tp-100) cc_final: 0.7617 (tm-30) REVERT: g 25 GLN cc_start: 0.7348 (tt0) cc_final: 0.7070 (tt0) REVERT: g 85 GLU cc_start: 0.8064 (tt0) cc_final: 0.7775 (tt0) REVERT: g 117 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7002 (tm-30) REVERT: h 15 LEU cc_start: 0.8178 (mm) cc_final: 0.7513 (pp) REVERT: h 108 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8065 (tm-30) REVERT: h 114 MET cc_start: 0.7964 (mtt) cc_final: 0.7689 (mtt) REVERT: i 89 MET cc_start: 0.8484 (mmm) cc_final: 0.7859 (mtp) REVERT: j 43 ASP cc_start: 0.7605 (t0) cc_final: 0.6618 (t0) REVERT: j 45 ASP cc_start: 0.7989 (t0) cc_final: 0.7429 (t0) REVERT: l 34 GLU cc_start: 0.7837 (pp20) cc_final: 0.7181 (pm20) REVERT: l 146 THR cc_start: 0.7011 (p) cc_final: 0.6754 (t) REVERT: m 84 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6085 (tttt) REVERT: m 112 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: n 11 HIS cc_start: 0.7345 (OUTLIER) cc_final: 0.7114 (t-90) REVERT: n 149 MET cc_start: 0.6820 (mtm) cc_final: 0.6540 (mtm) REVERT: o 38 MET cc_start: 0.7880 (tpp) cc_final: 0.7378 (mmm) REVERT: o 54 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: o 96 LYS cc_start: 0.8506 (mmtp) cc_final: 0.7963 (mtmt) REVERT: p 31 TYR cc_start: 0.7237 (t80) cc_final: 0.6840 (t80) REVERT: q 53 LYS cc_start: 0.9192 (mppt) cc_final: 0.8753 (mppt) REVERT: q 61 TRP cc_start: 0.9263 (p90) cc_final: 0.8368 (p90) REVERT: q 67 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: q 122 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7580 (tm-30) REVERT: r 69 MET cc_start: 0.4540 (OUTLIER) cc_final: 0.4266 (mtp) REVERT: r 112 LEU cc_start: 0.7390 (tt) cc_final: 0.6552 (mt) outliers start: 361 outliers final: 238 residues processed: 1581 average time/residue: 0.5765 time to fit residues: 1583.4616 Evaluate side-chains 1521 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1249 time to evaluate : 5.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 373 ASN Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain G residue 30 CYS Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 262 TRP Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 546 GLN Chi-restraints excluded: chain G residue 570 SER Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 42 MET Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 316 THR Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 286 ILE Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 298 ILE Chi-restraints excluded: chain M residue 314 MET Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 360 LEU Chi-restraints excluded: chain M residue 361 MET Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 148 LEU Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 164 MET Chi-restraints excluded: chain N residue 243 MET Chi-restraints excluded: chain N residue 244 ILE Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 335 MET Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 215 SER Chi-restraints excluded: chain O residue 226 TRP Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 176 ASP Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 27 LEU Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 65 CYS Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Y residue 23 ILE Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Z residue 49 MET Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 34 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 52 SER Chi-restraints excluded: chain j residue 59 TRP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 27 ASN Chi-restraints excluded: chain l residue 28 MET Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 113 PHE Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain l residue 153 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 82 THR Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 146 ASP Chi-restraints excluded: chain n residue 150 THR Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 54 GLN Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 90 GLU Chi-restraints excluded: chain p residue 9 TYR Chi-restraints excluded: chain p residue 74 THR Chi-restraints excluded: chain p residue 104 ILE Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain p residue 163 LEU Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 62 VAL Chi-restraints excluded: chain q residue 67 GLU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain s residue 31 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 735 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 chunk 434 optimal weight: 6.9990 chunk 556 optimal weight: 9.9990 chunk 431 optimal weight: 8.9990 chunk 641 optimal weight: 0.9990 chunk 425 optimal weight: 0.8980 chunk 759 optimal weight: 8.9990 chunk 475 optimal weight: 9.9990 chunk 463 optimal weight: 0.7980 chunk 350 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN C 53 HIS ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN ** M 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 184 ASN P 203 GLN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 GLN a 27 HIS ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN n 11 HIS ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 GLN ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 130 GLN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 35 GLN ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.279 66577 Z= 0.547 Angle : 1.662 51.062 90329 Z= 1.053 Chirality : 0.312 6.443 9974 Planarity : 0.005 0.098 11402 Dihedral : 7.682 175.693 8913 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.81 % Favored : 88.05 % Rotamer: Outliers : 4.02 % Allowed : 22.66 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.09), residues: 7951 helix: -0.67 (0.08), residues: 3768 sheet: -2.48 (0.26), residues: 400 loop : -2.88 (0.10), residues: 3783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 487 HIS 0.010 0.001 HIS P 3 PHE 0.028 0.001 PHE Y 60 TYR 0.038 0.002 TYR C 209 ARG 0.008 0.000 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1404 time to evaluate : 5.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.7858 (tmt) cc_final: 0.7615 (tmt) REVERT: B 68 GLU cc_start: 0.8045 (tp30) cc_final: 0.7766 (tp30) REVERT: B 126 MET cc_start: 0.7900 (ttm) cc_final: 0.7511 (ttp) REVERT: B 131 ASN cc_start: 0.8533 (m-40) cc_final: 0.8160 (m110) REVERT: B 135 TYR cc_start: 0.8133 (m-80) cc_final: 0.7912 (t80) REVERT: C 39 GLN cc_start: 0.8695 (pp30) cc_final: 0.8401 (pp30) REVERT: C 77 ASP cc_start: 0.7656 (m-30) cc_final: 0.7325 (m-30) REVERT: C 91 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: C 95 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8413 (m-40) REVERT: D 23 LYS cc_start: 0.7837 (ptpp) cc_final: 0.6767 (tptp) REVERT: D 35 ASP cc_start: 0.6962 (t70) cc_final: 0.6195 (t0) REVERT: D 72 MET cc_start: 0.7507 (tpp) cc_final: 0.7305 (tpp) REVERT: D 172 GLU cc_start: 0.7180 (tp30) cc_final: 0.6908 (tp30) REVERT: D 189 MET cc_start: 0.8035 (ttt) cc_final: 0.7702 (ttp) REVERT: D 342 MET cc_start: 0.8795 (mmm) cc_final: 0.8342 (tpp) REVERT: D 373 GLU cc_start: 0.7234 (tt0) cc_final: 0.6747 (tt0) REVERT: D 410 MET cc_start: 0.7565 (mtm) cc_final: 0.7352 (mtm) REVERT: E 9 HIS cc_start: 0.7086 (t-170) cc_final: 0.6839 (t-90) REVERT: E 74 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.6753 (mp10) REVERT: E 82 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7412 (mm-30) REVERT: E 101 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8380 (mt0) REVERT: F 50 LEU cc_start: 0.8125 (mt) cc_final: 0.7198 (tp) REVERT: F 82 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7646 (ppp) REVERT: F 272 MET cc_start: 0.9052 (tpt) cc_final: 0.8403 (tpt) REVERT: F 326 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7883 (mm110) REVERT: F 388 GLU cc_start: 0.7634 (mp0) cc_final: 0.7203 (mp0) REVERT: G 54 MET cc_start: 0.8581 (tpt) cc_final: 0.8161 (tpt) REVERT: G 94 MET cc_start: 0.8682 (mmm) cc_final: 0.8293 (mmm) REVERT: G 107 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8204 (mm) REVERT: G 122 MET cc_start: 0.8388 (mmp) cc_final: 0.8046 (mmp) REVERT: G 131 LEU cc_start: 0.8537 (pt) cc_final: 0.7950 (tt) REVERT: G 187 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8004 (pt) REVERT: G 192 MET cc_start: 0.7017 (ptm) cc_final: 0.6810 (ptm) REVERT: G 504 ASP cc_start: 0.8209 (m-30) cc_final: 0.7880 (t70) REVERT: G 512 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: G 546 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7713 (pp30) REVERT: G 556 MET cc_start: 0.8320 (ppp) cc_final: 0.7971 (ppp) REVERT: H 59 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6182 (mm-30) REVERT: H 61 MET cc_start: 0.5574 (pmm) cc_final: 0.5161 (pmm) REVERT: H 150 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8779 (tm) REVERT: H 155 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9078 (tm) REVERT: H 195 ARG cc_start: 0.7239 (tpt90) cc_final: 0.7033 (tpt90) REVERT: I 16 MET cc_start: 0.6254 (tmt) cc_final: 0.5810 (tmt) REVERT: I 22 ASN cc_start: 0.7949 (t0) cc_final: 0.7563 (t0) REVERT: I 25 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7809 (ttm-80) REVERT: I 28 MET cc_start: 0.7826 (tpt) cc_final: 0.7180 (tpt) REVERT: I 38 MET cc_start: 0.7973 (tmm) cc_final: 0.7658 (tmm) REVERT: I 96 ILE cc_start: 0.7802 (mp) cc_final: 0.7574 (mp) REVERT: I 110 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7714 (ttp80) REVERT: I 166 GLU cc_start: 0.8238 (tt0) cc_final: 0.8034 (tt0) REVERT: I 174 ASP cc_start: 0.7568 (t70) cc_final: 0.7119 (t0) REVERT: J 153 VAL cc_start: 0.7845 (OUTLIER) cc_final: 0.7555 (p) REVERT: K 21 MET cc_start: 0.7421 (mmm) cc_final: 0.6728 (ptm) REVERT: K 23 ARG cc_start: 0.6713 (mtp-110) cc_final: 0.5624 (mmt180) REVERT: K 36 MET cc_start: 0.7906 (ttm) cc_final: 0.7669 (ttm) REVERT: K 62 THR cc_start: 0.9143 (m) cc_final: 0.8792 (m) REVERT: K 97 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8159 (pm20) REVERT: L 150 MET cc_start: 0.8109 (ttm) cc_final: 0.7805 (ttm) REVERT: L 197 GLU cc_start: 0.8664 (pt0) cc_final: 0.8161 (pt0) REVERT: L 261 VAL cc_start: 0.8702 (m) cc_final: 0.8457 (p) REVERT: L 335 PHE cc_start: 0.8144 (m-10) cc_final: 0.7870 (m-80) REVERT: L 352 ASP cc_start: 0.6658 (t70) cc_final: 0.6334 (t0) REVERT: L 383 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7633 (mmp) REVERT: L 400 ASN cc_start: 0.7721 (p0) cc_final: 0.6649 (t0) REVERT: L 418 MET cc_start: 0.8603 (mtp) cc_final: 0.8175 (ttm) REVERT: L 503 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7600 (mm-30) REVERT: L 587 TYR cc_start: 0.8808 (m-10) cc_final: 0.8156 (m-10) REVERT: M 2 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8557 (tt) REVERT: M 177 MET cc_start: 0.7892 (ppp) cc_final: 0.7632 (ppp) REVERT: M 216 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8590 (tm) REVERT: M 276 CYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7766 (t) REVERT: M 286 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7978 (mp) REVERT: M 310 MET cc_start: 0.7987 (tpt) cc_final: 0.7689 (tpt) REVERT: M 315 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8559 (tm) REVERT: M 355 MET cc_start: 0.7846 (tpp) cc_final: 0.7576 (tpp) REVERT: M 376 MET cc_start: 0.8166 (mtp) cc_final: 0.7883 (ttt) REVERT: M 415 GLN cc_start: 0.8596 (mp10) cc_final: 0.8177 (mp10) REVERT: M 459 MET cc_start: 0.6659 (mmt) cc_final: 0.3748 (tpt) REVERT: N 79 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8344 (tppt) REVERT: N 282 MET cc_start: 0.7689 (mtp) cc_final: 0.7309 (mtm) REVERT: O 81 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8254 (tmmt) REVERT: O 131 ASP cc_start: 0.7960 (t70) cc_final: 0.7321 (t70) REVERT: O 214 MET cc_start: 0.7993 (tpp) cc_final: 0.7683 (tpp) REVERT: O 271 ASN cc_start: 0.7778 (m-40) cc_final: 0.7444 (t0) REVERT: P 57 MET cc_start: 0.8628 (tpp) cc_final: 0.8311 (mmt) REVERT: P 82 ARG cc_start: 0.8432 (tpt-90) cc_final: 0.7846 (tmm160) REVERT: P 244 TYR cc_start: 0.8060 (t80) cc_final: 0.7696 (t80) REVERT: Q 39 VAL cc_start: 0.8948 (t) cc_final: 0.8675 (m) REVERT: Q 57 MET cc_start: 0.8682 (tmm) cc_final: 0.8419 (tmm) REVERT: R 22 ASP cc_start: 0.7461 (m-30) cc_final: 0.7111 (m-30) REVERT: R 57 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7332 (tp) REVERT: R 72 TYR cc_start: 0.8552 (m-80) cc_final: 0.8211 (m-80) REVERT: S 39 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7430 (ttp-170) REVERT: T 21 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7743 (pp) REVERT: T 76 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8081 (mm) REVERT: U 37 MET cc_start: 0.5860 (mmp) cc_final: 0.5627 (mmm) REVERT: U 66 ASP cc_start: 0.7774 (m-30) cc_final: 0.7564 (m-30) REVERT: U 74 GLN cc_start: 0.8591 (tp40) cc_final: 0.8170 (tp40) REVERT: U 79 TYR cc_start: 0.8173 (t80) cc_final: 0.7881 (t80) REVERT: V 57 MET cc_start: 0.8677 (ptp) cc_final: 0.8332 (ptp) REVERT: V 81 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7986 (tm) REVERT: V 95 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8151 (pttt) REVERT: V 96 TRP cc_start: 0.6448 (m-10) cc_final: 0.5869 (m-10) REVERT: W 44 GLU cc_start: 0.8427 (tt0) cc_final: 0.7741 (tt0) REVERT: W 96 ILE cc_start: 0.8631 (tt) cc_final: 0.8363 (tp) REVERT: X 43 MET cc_start: 0.8642 (mmm) cc_final: 0.8433 (mmp) REVERT: X 47 TRP cc_start: 0.7591 (m100) cc_final: 0.7372 (m100) REVERT: Y 41 SER cc_start: 0.9015 (p) cc_final: 0.8723 (t) REVERT: Y 71 LEU cc_start: 0.8640 (tp) cc_final: 0.8385 (tp) REVERT: Y 125 LYS cc_start: 0.8516 (ttmm) cc_final: 0.7972 (ttmm) REVERT: Z 32 TYR cc_start: 0.6437 (m-10) cc_final: 0.5576 (m-10) REVERT: Z 60 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8492 (tt) REVERT: Z 124 TYR cc_start: 0.6782 (p90) cc_final: 0.6510 (p90) REVERT: Z 132 MET cc_start: 0.8020 (tpp) cc_final: 0.7131 (tpp) REVERT: a 1 MET cc_start: 0.7088 (mmm) cc_final: 0.6828 (mmm) REVERT: a 44 GLN cc_start: 0.8660 (mt0) cc_final: 0.8343 (pt0) REVERT: b 46 LYS cc_start: 0.8604 (tttm) cc_final: 0.8177 (tttt) REVERT: b 81 LYS cc_start: 0.8312 (mppt) cc_final: 0.7845 (mppt) REVERT: b 82 ASN cc_start: 0.7377 (t0) cc_final: 0.7052 (t0) REVERT: d 2 MET cc_start: 0.8058 (mmm) cc_final: 0.7844 (mmp) REVERT: d 14 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6377 (tp) REVERT: d 36 LEU cc_start: 0.8263 (mt) cc_final: 0.7818 (tp) REVERT: d 43 LEU cc_start: 0.8925 (tp) cc_final: 0.8603 (tp) REVERT: d 58 LEU cc_start: 0.7463 (mm) cc_final: 0.7227 (mm) REVERT: d 95 LYS cc_start: 0.9161 (tmmt) cc_final: 0.8523 (ttmt) REVERT: d 111 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: e 3 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7985 (tm) REVERT: e 18 MET cc_start: 0.8157 (mmm) cc_final: 0.7742 (mmm) REVERT: e 61 ASP cc_start: 0.8541 (p0) cc_final: 0.8264 (p0) REVERT: e 98 SER cc_start: 0.7996 (m) cc_final: 0.7468 (p) REVERT: f 24 TYR cc_start: 0.7954 (t80) cc_final: 0.7638 (t80) REVERT: f 30 ASP cc_start: 0.7422 (m-30) cc_final: 0.7084 (m-30) REVERT: g 23 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7585 (tm-30) REVERT: g 25 GLN cc_start: 0.7180 (tt0) cc_final: 0.6931 (tt0) REVERT: g 85 GLU cc_start: 0.7989 (tt0) cc_final: 0.7717 (tt0) REVERT: g 117 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7094 (tm-30) REVERT: h 15 LEU cc_start: 0.7929 (mm) cc_final: 0.7519 (mt) REVERT: h 108 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8067 (tm-30) REVERT: h 114 MET cc_start: 0.7884 (mtt) cc_final: 0.7579 (mtt) REVERT: j 39 ARG cc_start: 0.6938 (tpp80) cc_final: 0.6426 (tpp-160) REVERT: j 43 ASP cc_start: 0.7367 (t0) cc_final: 0.6541 (t0) REVERT: j 45 ASP cc_start: 0.7872 (t0) cc_final: 0.7373 (t0) REVERT: l 34 GLU cc_start: 0.7818 (pp20) cc_final: 0.7094 (pm20) REVERT: m 49 GLN cc_start: 0.8891 (tt0) cc_final: 0.8481 (mt0) REVERT: m 84 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6081 (tttt) REVERT: m 112 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: n 56 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7476 (mmp) REVERT: n 74 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8325 (pp30) REVERT: n 149 MET cc_start: 0.6698 (mtm) cc_final: 0.6463 (mtm) REVERT: n 153 LEU cc_start: 0.5560 (mm) cc_final: 0.5267 (mt) REVERT: o 38 MET cc_start: 0.7749 (tpp) cc_final: 0.7194 (mmm) REVERT: o 96 LYS cc_start: 0.8451 (mmtp) cc_final: 0.7969 (mtmt) REVERT: p 31 TYR cc_start: 0.7175 (t80) cc_final: 0.6783 (t80) REVERT: p 99 GLN cc_start: 0.8277 (tt0) cc_final: 0.8045 (mt0) REVERT: q 61 TRP cc_start: 0.9237 (p90) cc_final: 0.8418 (p90) REVERT: q 122 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7556 (tm-30) REVERT: r 112 LEU cc_start: 0.7279 (tt) cc_final: 0.6612 (mt) outliers start: 282 outliers final: 175 residues processed: 1574 average time/residue: 0.5901 time to fit residues: 1609.0692 Evaluate side-chains 1477 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1267 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 146 CYS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain G residue 30 CYS Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 488 LYS Chi-restraints excluded: chain G residue 512 GLU Chi-restraints excluded: chain G residue 546 GLN Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain H residue 318 MET Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 110 ARG Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 42 PHE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 196 TRP Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 286 ILE Chi-restraints excluded: chain M residue 314 MET Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 360 LEU Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 196 TYR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 226 TRP Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain V residue 93 MET Chi-restraints excluded: chain W residue 18 SER Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 65 CYS Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain g residue 110 TYR Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 59 TRP Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 27 ASN Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 56 MET Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 73 ASN Chi-restraints excluded: chain n residue 74 GLN Chi-restraints excluded: chain n residue 146 ASP Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 90 GLU Chi-restraints excluded: chain p residue 9 TYR Chi-restraints excluded: chain p residue 128 LEU Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain q residue 141 SER Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain s residue 51 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 469 optimal weight: 4.9990 chunk 303 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 482 optimal weight: 9.9990 chunk 517 optimal weight: 0.7980 chunk 375 optimal weight: 0.0010 chunk 70 optimal weight: 0.9990 chunk 596 optimal weight: 0.0670 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 581 GLN G 582 GLN G 629 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 HIS ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 180 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 108 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 117 HIS ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 108 GLN l 27 ASN n 11 HIS ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 103 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.275 66577 Z= 0.547 Angle : 1.662 51.074 90329 Z= 1.053 Chirality : 0.311 6.445 9974 Planarity : 0.005 0.097 11402 Dihedral : 7.495 173.170 8913 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.71 % Favored : 88.15 % Rotamer: Outliers : 3.79 % Allowed : 23.44 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.09), residues: 7951 helix: -0.51 (0.09), residues: 3737 sheet: -2.33 (0.27), residues: 384 loop : -2.80 (0.10), residues: 3830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP F 291 HIS 0.028 0.001 HIS n 11 PHE 0.034 0.001 PHE D 168 TYR 0.036 0.002 TYR C 209 ARG 0.008 0.000 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1394 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.7957 (tmt) cc_final: 0.7727 (tmt) REVERT: B 126 MET cc_start: 0.7803 (ttm) cc_final: 0.7408 (ttt) REVERT: B 131 ASN cc_start: 0.8451 (m-40) cc_final: 0.8122 (m110) REVERT: C 39 GLN cc_start: 0.8648 (pp30) cc_final: 0.8344 (pp30) REVERT: C 77 ASP cc_start: 0.7754 (m-30) cc_final: 0.7466 (m-30) REVERT: C 95 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8490 (m-40) REVERT: C 199 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (pp) REVERT: D 23 LYS cc_start: 0.7637 (ptpp) cc_final: 0.6932 (tptp) REVERT: D 35 ASP cc_start: 0.6990 (t70) cc_final: 0.6221 (t0) REVERT: D 72 MET cc_start: 0.7695 (tpp) cc_final: 0.7478 (tpp) REVERT: D 172 GLU cc_start: 0.7092 (tp30) cc_final: 0.6797 (tp30) REVERT: D 189 MET cc_start: 0.7945 (ttt) cc_final: 0.7433 (ttt) REVERT: D 342 MET cc_start: 0.8745 (mmm) cc_final: 0.8219 (tpp) REVERT: D 373 GLU cc_start: 0.7242 (tt0) cc_final: 0.6786 (tt0) REVERT: D 410 MET cc_start: 0.7526 (mtm) cc_final: 0.7190 (mtm) REVERT: E 9 HIS cc_start: 0.6967 (t-170) cc_final: 0.6684 (t-90) REVERT: E 82 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7435 (mm-30) REVERT: E 101 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: F 50 LEU cc_start: 0.8034 (mt) cc_final: 0.7136 (tp) REVERT: F 82 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6974 (ppp) REVERT: F 129 MET cc_start: 0.6928 (ttm) cc_final: 0.6647 (ttm) REVERT: F 272 MET cc_start: 0.9076 (tpt) cc_final: 0.8481 (tpt) REVERT: F 326 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7910 (mm110) REVERT: F 388 GLU cc_start: 0.7608 (mp0) cc_final: 0.7189 (mp0) REVERT: G 54 MET cc_start: 0.8553 (tpt) cc_final: 0.8128 (tpt) REVERT: G 107 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8238 (mm) REVERT: G 122 MET cc_start: 0.8474 (mmp) cc_final: 0.8172 (mmp) REVERT: G 131 LEU cc_start: 0.8486 (pt) cc_final: 0.7962 (tt) REVERT: G 187 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7823 (pp) REVERT: G 192 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.7009 (ptp) REVERT: G 504 ASP cc_start: 0.8193 (m-30) cc_final: 0.7888 (t70) REVERT: G 556 MET cc_start: 0.8336 (ppp) cc_final: 0.8081 (ppp) REVERT: H 17 MET cc_start: 0.8176 (tmm) cc_final: 0.7864 (tmm) REVERT: H 59 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6017 (mm-30) REVERT: H 61 MET cc_start: 0.5197 (pmm) cc_final: 0.4936 (pmm) REVERT: H 143 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7852 (tt0) REVERT: I 16 MET cc_start: 0.6164 (tmt) cc_final: 0.5773 (tmt) REVERT: I 22 ASN cc_start: 0.7975 (t0) cc_final: 0.7534 (t0) REVERT: I 25 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7813 (ttm-80) REVERT: I 28 MET cc_start: 0.7712 (tpt) cc_final: 0.7356 (tpt) REVERT: I 32 LEU cc_start: 0.8117 (mt) cc_final: 0.7468 (mp) REVERT: I 38 MET cc_start: 0.8120 (tmm) cc_final: 0.7792 (tmm) REVERT: I 96 ILE cc_start: 0.7803 (mp) cc_final: 0.7580 (mp) REVERT: I 110 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7848 (ttp80) REVERT: I 166 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: I 174 ASP cc_start: 0.7633 (t70) cc_final: 0.7208 (t0) REVERT: K 21 MET cc_start: 0.7328 (mmm) cc_final: 0.6697 (ptm) REVERT: K 23 ARG cc_start: 0.6694 (mtp-110) cc_final: 0.5559 (mmt180) REVERT: K 97 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: L 150 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7777 (ttm) REVERT: L 201 ILE cc_start: 0.8835 (mt) cc_final: 0.8400 (mt) REVERT: L 261 VAL cc_start: 0.8670 (m) cc_final: 0.8401 (p) REVERT: L 352 ASP cc_start: 0.6634 (t70) cc_final: 0.6323 (t0) REVERT: L 366 MET cc_start: 0.8053 (mtm) cc_final: 0.7637 (mtm) REVERT: L 378 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7938 (tt) REVERT: L 381 THR cc_start: 0.7891 (p) cc_final: 0.7686 (p) REVERT: L 383 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.6552 (mmm) REVERT: L 503 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7586 (mm-30) REVERT: L 587 TYR cc_start: 0.8814 (m-10) cc_final: 0.8135 (m-10) REVERT: M 2 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8573 (tt) REVERT: M 66 ILE cc_start: 0.9428 (mm) cc_final: 0.9153 (mt) REVERT: M 177 MET cc_start: 0.7815 (ppp) cc_final: 0.7507 (ppp) REVERT: M 216 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8576 (tm) REVERT: M 276 CYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7832 (t) REVERT: M 278 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.6921 (ttp80) REVERT: M 286 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7983 (mp) REVERT: M 315 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8504 (tm) REVERT: M 329 LEU cc_start: 0.9251 (mm) cc_final: 0.8991 (mp) REVERT: M 355 MET cc_start: 0.7903 (tpp) cc_final: 0.7631 (tpp) REVERT: M 376 MET cc_start: 0.8167 (mtp) cc_final: 0.7803 (ttp) REVERT: M 459 MET cc_start: 0.6527 (mmt) cc_final: 0.3683 (tpt) REVERT: N 79 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8163 (tppt) REVERT: N 314 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7434 (ttp) REVERT: O 81 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8095 (tmmt) REVERT: O 131 ASP cc_start: 0.7913 (t70) cc_final: 0.7310 (t70) REVERT: O 214 MET cc_start: 0.8078 (tpp) cc_final: 0.7701 (tpp) REVERT: O 271 ASN cc_start: 0.7670 (m-40) cc_final: 0.7114 (m-40) REVERT: P 57 MET cc_start: 0.8628 (tpp) cc_final: 0.8286 (mmt) REVERT: P 82 ARG cc_start: 0.8418 (tpt-90) cc_final: 0.7820 (tmm160) REVERT: Q 39 VAL cc_start: 0.8928 (t) cc_final: 0.8663 (m) REVERT: Q 63 GLU cc_start: 0.7409 (tt0) cc_final: 0.7064 (pt0) REVERT: R 22 ASP cc_start: 0.7410 (m-30) cc_final: 0.7084 (m-30) REVERT: R 57 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7262 (tp) REVERT: R 72 TYR cc_start: 0.8533 (m-80) cc_final: 0.8147 (m-80) REVERT: S 34 ASP cc_start: 0.8492 (m-30) cc_final: 0.7178 (t70) REVERT: S 39 ARG cc_start: 0.7706 (ttp-170) cc_final: 0.7469 (ttp-170) REVERT: T 21 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7659 (pp) REVERT: T 76 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8006 (mm) REVERT: U 46 ASP cc_start: 0.7438 (t0) cc_final: 0.7184 (t70) REVERT: U 74 GLN cc_start: 0.8588 (tp40) cc_final: 0.8235 (tp40) REVERT: U 79 TYR cc_start: 0.8123 (t80) cc_final: 0.7792 (t80) REVERT: V 57 MET cc_start: 0.8699 (ptp) cc_final: 0.8326 (ptp) REVERT: V 81 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7885 (tm) REVERT: V 86 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7711 (pm20) REVERT: V 95 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8238 (pttt) REVERT: V 96 TRP cc_start: 0.6606 (m-10) cc_final: 0.5991 (m-10) REVERT: W 44 GLU cc_start: 0.8351 (tt0) cc_final: 0.7707 (tt0) REVERT: W 96 ILE cc_start: 0.8570 (tt) cc_final: 0.8343 (tp) REVERT: X 47 TRP cc_start: 0.7511 (m100) cc_final: 0.7243 (m100) REVERT: Y 41 SER cc_start: 0.8961 (p) cc_final: 0.8628 (t) REVERT: Y 71 LEU cc_start: 0.8547 (tp) cc_final: 0.8182 (tp) REVERT: Y 125 LYS cc_start: 0.8515 (ttmm) cc_final: 0.7887 (tttm) REVERT: Z 60 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (tt) REVERT: Z 124 TYR cc_start: 0.6803 (p90) cc_final: 0.6545 (p90) REVERT: Z 132 MET cc_start: 0.7727 (tpp) cc_final: 0.6843 (tpp) REVERT: a 1 MET cc_start: 0.6741 (mmm) cc_final: 0.6409 (mmm) REVERT: a 44 GLN cc_start: 0.8668 (mt0) cc_final: 0.8304 (pt0) REVERT: b 46 LYS cc_start: 0.8595 (tttm) cc_final: 0.8200 (tttt) REVERT: b 62 MET cc_start: 0.6706 (ptp) cc_final: 0.6301 (pmm) REVERT: b 82 ASN cc_start: 0.7109 (t0) cc_final: 0.6735 (t0) REVERT: d 2 MET cc_start: 0.8104 (mmm) cc_final: 0.7786 (mmp) REVERT: d 14 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6214 (tp) REVERT: d 36 LEU cc_start: 0.8194 (mt) cc_final: 0.7712 (tp) REVERT: d 43 LEU cc_start: 0.8890 (tp) cc_final: 0.8585 (tp) REVERT: d 95 LYS cc_start: 0.9151 (tmmt) cc_final: 0.8515 (ttmt) REVERT: d 106 LYS cc_start: 0.6013 (mttt) cc_final: 0.5593 (mttt) REVERT: d 111 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: e 3 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7989 (tm) REVERT: e 18 MET cc_start: 0.8218 (mmm) cc_final: 0.7785 (mmm) REVERT: e 98 SER cc_start: 0.8031 (m) cc_final: 0.7459 (p) REVERT: f 24 TYR cc_start: 0.7923 (t80) cc_final: 0.7612 (t80) REVERT: f 30 ASP cc_start: 0.7438 (m-30) cc_final: 0.7046 (m-30) REVERT: g 23 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7539 (tm-30) REVERT: g 25 GLN cc_start: 0.7078 (tt0) cc_final: 0.6851 (tt0) REVERT: g 85 GLU cc_start: 0.7983 (tt0) cc_final: 0.7702 (tt0) REVERT: g 117 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7480 (tm-30) REVERT: h 15 LEU cc_start: 0.7811 (mm) cc_final: 0.7435 (mt) REVERT: h 59 TYR cc_start: 0.7879 (t80) cc_final: 0.7551 (t80) REVERT: h 114 MET cc_start: 0.7949 (mtt) cc_final: 0.7673 (mtt) REVERT: j 34 PHE cc_start: 0.8712 (t80) cc_final: 0.8437 (t80) REVERT: j 39 ARG cc_start: 0.6815 (tpp80) cc_final: 0.6426 (tpp-160) REVERT: j 43 ASP cc_start: 0.7451 (t0) cc_final: 0.6789 (t0) REVERT: j 45 ASP cc_start: 0.7782 (t0) cc_final: 0.7454 (t0) REVERT: k 58 TYR cc_start: 0.8132 (m-10) cc_final: 0.7869 (m-80) REVERT: l 34 GLU cc_start: 0.7780 (pp20) cc_final: 0.6874 (pm20) REVERT: l 48 MET cc_start: 0.6954 (mmm) cc_final: 0.5359 (mmm) REVERT: m 34 GLU cc_start: 0.7780 (tt0) cc_final: 0.7269 (mt-10) REVERT: m 84 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.6084 (tttt) REVERT: m 112 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: n 149 MET cc_start: 0.6551 (mtm) cc_final: 0.6248 (mtm) REVERT: n 153 LEU cc_start: 0.5367 (mm) cc_final: 0.5083 (mt) REVERT: o 38 MET cc_start: 0.7753 (tpp) cc_final: 0.7360 (mmm) REVERT: o 96 LYS cc_start: 0.8446 (mmtp) cc_final: 0.7859 (mtmt) REVERT: p 31 TYR cc_start: 0.7124 (t80) cc_final: 0.6773 (t80) REVERT: q 41 GLU cc_start: 0.7947 (tp30) cc_final: 0.7447 (tp30) REVERT: q 61 TRP cc_start: 0.9208 (p90) cc_final: 0.8457 (p90) REVERT: q 122 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7524 (tm-30) REVERT: r 112 LEU cc_start: 0.7227 (tt) cc_final: 0.6622 (mt) outliers start: 266 outliers final: 169 residues processed: 1545 average time/residue: 0.5691 time to fit residues: 1524.7477 Evaluate side-chains 1482 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1279 time to evaluate : 5.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 130 PHE Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 110 ARG Chi-restraints excluded: chain I residue 149 LEU Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 42 PHE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 330 CYS Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 286 ILE Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 360 LEU Chi-restraints excluded: chain M residue 361 MET Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 19 ILE Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 98 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 196 TYR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 314 MET Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 226 TRP Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 65 CYS Chi-restraints excluded: chain X residue 82 THR Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 87 LEU Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 27 ASN Chi-restraints excluded: chain l residue 127 VAL Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 146 ASP Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 90 GLU Chi-restraints excluded: chain p residue 128 LEU Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 69 MET Chi-restraints excluded: chain r residue 101 LYS Chi-restraints excluded: chain r residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 690 optimal weight: 3.9990 chunk 727 optimal weight: 7.9990 chunk 663 optimal weight: 1.9990 chunk 707 optimal weight: 0.9980 chunk 425 optimal weight: 0.6980 chunk 308 optimal weight: 2.9990 chunk 555 optimal weight: 0.0020 chunk 217 optimal weight: 3.9990 chunk 639 optimal weight: 0.9990 chunk 669 optimal weight: 10.0000 chunk 705 optimal weight: 0.0030 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 ASN ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS l 27 ASN n 11 HIS ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 60 HIS ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.274 66577 Z= 0.547 Angle : 1.664 51.053 90329 Z= 1.053 Chirality : 0.311 6.438 9974 Planarity : 0.005 0.096 11402 Dihedral : 7.347 175.291 8913 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.65 % Favored : 88.23 % Rotamer: Outliers : 3.43 % Allowed : 24.14 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.09), residues: 7951 helix: -0.37 (0.09), residues: 3704 sheet: -2.34 (0.27), residues: 385 loop : -2.75 (0.10), residues: 3862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 291 HIS 0.020 0.001 HIS f 9 PHE 0.033 0.001 PHE D 171 TYR 0.032 0.001 TYR C 209 ARG 0.007 0.000 ARG l 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1654 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1413 time to evaluate : 5.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.7917 (tmt) cc_final: 0.7706 (tmt) REVERT: B 126 MET cc_start: 0.7767 (ttm) cc_final: 0.7455 (ttt) REVERT: C 39 GLN cc_start: 0.8576 (pp30) cc_final: 0.8288 (pp30) REVERT: C 69 ASN cc_start: 0.8171 (m-40) cc_final: 0.7894 (t0) REVERT: C 77 ASP cc_start: 0.7739 (m-30) cc_final: 0.7444 (m-30) REVERT: C 199 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (pp) REVERT: D 23 LYS cc_start: 0.7484 (ptpp) cc_final: 0.6783 (tptp) REVERT: D 35 ASP cc_start: 0.6973 (t70) cc_final: 0.6196 (t0) REVERT: D 72 MET cc_start: 0.7744 (tpp) cc_final: 0.7501 (tpp) REVERT: D 157 HIS cc_start: 0.7924 (t-170) cc_final: 0.7579 (t-170) REVERT: D 172 GLU cc_start: 0.7163 (tp30) cc_final: 0.6934 (tp30) REVERT: D 189 MET cc_start: 0.7929 (ttt) cc_final: 0.7481 (ttt) REVERT: D 342 MET cc_start: 0.8748 (mmm) cc_final: 0.8221 (tpp) REVERT: D 373 GLU cc_start: 0.7211 (tt0) cc_final: 0.6805 (tt0) REVERT: D 410 MET cc_start: 0.7495 (mtm) cc_final: 0.7140 (mtm) REVERT: E 9 HIS cc_start: 0.6893 (t-170) cc_final: 0.6642 (t-90) REVERT: E 82 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7318 (mm-30) REVERT: E 101 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: F 50 LEU cc_start: 0.8020 (mt) cc_final: 0.7129 (tp) REVERT: F 82 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7191 (ppp) REVERT: F 99 GLU cc_start: 0.7272 (mp0) cc_final: 0.6948 (mp0) REVERT: F 129 MET cc_start: 0.7003 (ttm) cc_final: 0.6689 (ttm) REVERT: F 272 MET cc_start: 0.9077 (tpt) cc_final: 0.8499 (tpt) REVERT: F 326 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7839 (mm110) REVERT: F 388 GLU cc_start: 0.7583 (mp0) cc_final: 0.7169 (mp0) REVERT: G 54 MET cc_start: 0.8496 (tpt) cc_final: 0.8147 (tpt) REVERT: G 94 MET cc_start: 0.8698 (mmm) cc_final: 0.8194 (tpp) REVERT: G 107 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8161 (mm) REVERT: G 122 MET cc_start: 0.8396 (mmp) cc_final: 0.8153 (mmp) REVERT: G 131 LEU cc_start: 0.8476 (pt) cc_final: 0.7957 (tt) REVERT: G 187 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7830 (pp) REVERT: G 504 ASP cc_start: 0.8109 (m-30) cc_final: 0.7876 (t70) REVERT: G 556 MET cc_start: 0.8448 (ppp) cc_final: 0.8190 (ppp) REVERT: G 568 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7997 (mp0) REVERT: G 684 MET cc_start: 0.8412 (mmp) cc_final: 0.8046 (mmt) REVERT: H 31 MET cc_start: 0.8650 (mtp) cc_final: 0.8064 (mtp) REVERT: H 59 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6160 (mm-30) REVERT: H 143 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7809 (tt0) REVERT: H 230 ASN cc_start: 0.8370 (m-40) cc_final: 0.8081 (t0) REVERT: H 271 LEU cc_start: 0.8374 (mm) cc_final: 0.8024 (mt) REVERT: I 16 MET cc_start: 0.6047 (tmt) cc_final: 0.5664 (tmt) REVERT: I 22 ASN cc_start: 0.8021 (t0) cc_final: 0.7407 (t0) REVERT: I 25 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7693 (ttm-80) REVERT: I 28 MET cc_start: 0.7727 (tpt) cc_final: 0.7526 (tpt) REVERT: I 32 LEU cc_start: 0.8203 (mt) cc_final: 0.7559 (mp) REVERT: I 96 ILE cc_start: 0.7725 (mp) cc_final: 0.7457 (mp) REVERT: I 110 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7943 (ttp80) REVERT: I 166 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: I 174 ASP cc_start: 0.7643 (t70) cc_final: 0.7213 (t0) REVERT: J 135 LEU cc_start: 0.7349 (mp) cc_final: 0.7139 (tt) REVERT: K 21 MET cc_start: 0.7247 (mmm) cc_final: 0.6677 (ptm) REVERT: K 23 ARG cc_start: 0.6622 (mtp-110) cc_final: 0.5460 (mmt180) REVERT: K 97 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8092 (pm20) REVERT: L 137 MET cc_start: 0.7907 (ttp) cc_final: 0.7699 (ttp) REVERT: L 150 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7846 (ttm) REVERT: L 197 GLU cc_start: 0.8451 (pt0) cc_final: 0.7506 (pt0) REVERT: L 201 ILE cc_start: 0.8787 (mt) cc_final: 0.8339 (mt) REVERT: L 252 MET cc_start: 0.7766 (tmm) cc_final: 0.7541 (tmm) REVERT: L 261 VAL cc_start: 0.8664 (m) cc_final: 0.8309 (p) REVERT: L 335 PHE cc_start: 0.8120 (m-10) cc_final: 0.7848 (m-10) REVERT: L 352 ASP cc_start: 0.6600 (t70) cc_final: 0.6327 (t0) REVERT: L 378 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7595 (tt) REVERT: L 383 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6631 (mmm) REVERT: L 421 MET cc_start: 0.8412 (mpp) cc_final: 0.7414 (mpp) REVERT: L 486 LEU cc_start: 0.8782 (mt) cc_final: 0.8551 (tp) REVERT: L 503 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7578 (mm-30) REVERT: L 587 TYR cc_start: 0.8807 (m-10) cc_final: 0.8167 (m-10) REVERT: M 2 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8461 (tt) REVERT: M 30 TYR cc_start: 0.8074 (m-80) cc_final: 0.7569 (m-80) REVERT: M 66 ILE cc_start: 0.9420 (mm) cc_final: 0.9164 (mt) REVERT: M 177 MET cc_start: 0.7701 (ppp) cc_final: 0.7458 (ppp) REVERT: M 216 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8634 (tm) REVERT: M 276 CYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7859 (t) REVERT: M 286 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.7970 (mp) REVERT: M 310 MET cc_start: 0.7965 (tpt) cc_final: 0.7635 (tpt) REVERT: M 315 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8499 (tm) REVERT: M 329 LEU cc_start: 0.9219 (mm) cc_final: 0.8974 (mp) REVERT: M 355 MET cc_start: 0.7902 (tpp) cc_final: 0.7659 (tpp) REVERT: M 376 MET cc_start: 0.8221 (mtp) cc_final: 0.7832 (ttt) REVERT: M 439 LEU cc_start: 0.8695 (mt) cc_final: 0.8482 (mt) REVERT: M 459 MET cc_start: 0.6620 (mmt) cc_final: 0.3846 (tpt) REVERT: N 225 MET cc_start: 0.8152 (mpp) cc_final: 0.7927 (mpp) REVERT: O 30 ASN cc_start: 0.7665 (t0) cc_final: 0.7344 (m-40) REVERT: O 89 ASN cc_start: 0.6151 (m110) cc_final: 0.5870 (t0) REVERT: O 131 ASP cc_start: 0.7837 (t70) cc_final: 0.7244 (t70) REVERT: O 214 MET cc_start: 0.8016 (tpp) cc_final: 0.7687 (tpp) REVERT: O 271 ASN cc_start: 0.7572 (m-40) cc_final: 0.7059 (m-40) REVERT: P 57 MET cc_start: 0.8611 (tpp) cc_final: 0.8295 (mmt) REVERT: P 82 ARG cc_start: 0.8382 (tpt-90) cc_final: 0.7838 (tmm160) REVERT: Q 39 VAL cc_start: 0.8912 (t) cc_final: 0.8651 (m) REVERT: Q 63 GLU cc_start: 0.7457 (tt0) cc_final: 0.7160 (pt0) REVERT: R 22 ASP cc_start: 0.7435 (m-30) cc_final: 0.7088 (m-30) REVERT: R 57 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7207 (tp) REVERT: R 72 TYR cc_start: 0.8519 (m-80) cc_final: 0.8150 (m-80) REVERT: S 34 ASP cc_start: 0.8507 (m-30) cc_final: 0.7248 (t70) REVERT: S 39 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7625 (ttp-170) REVERT: S 56 GLU cc_start: 0.7060 (pm20) cc_final: 0.6776 (pp20) REVERT: T 21 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7644 (pp) REVERT: T 71 MET cc_start: 0.5339 (mmm) cc_final: 0.5100 (mmm) REVERT: U 46 ASP cc_start: 0.7347 (t0) cc_final: 0.7086 (t70) REVERT: U 74 GLN cc_start: 0.8598 (tp40) cc_final: 0.8201 (tp40) REVERT: V 57 MET cc_start: 0.8688 (ptp) cc_final: 0.8301 (ptp) REVERT: V 81 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7837 (tm) REVERT: V 86 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: V 95 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8230 (pttt) REVERT: V 96 TRP cc_start: 0.6588 (m-10) cc_final: 0.5951 (m-10) REVERT: W 44 GLU cc_start: 0.8367 (tt0) cc_final: 0.7708 (tt0) REVERT: W 90 MET cc_start: 0.8339 (mtt) cc_final: 0.8123 (ttm) REVERT: W 96 ILE cc_start: 0.8562 (tt) cc_final: 0.8329 (tp) REVERT: W 106 MET cc_start: 0.8717 (tpp) cc_final: 0.8427 (tpp) REVERT: Y 41 SER cc_start: 0.8939 (p) cc_final: 0.8635 (t) REVERT: Y 71 LEU cc_start: 0.8549 (tp) cc_final: 0.8208 (tp) REVERT: Y 125 LYS cc_start: 0.8477 (ttmm) cc_final: 0.7908 (ttmm) REVERT: Y 128 LYS cc_start: 0.8228 (tppt) cc_final: 0.7659 (tppt) REVERT: Z 60 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8483 (tt) REVERT: Z 124 TYR cc_start: 0.6820 (p90) cc_final: 0.6523 (p90) REVERT: Z 132 MET cc_start: 0.7597 (tpp) cc_final: 0.6989 (tpp) REVERT: a 1 MET cc_start: 0.6809 (mmm) cc_final: 0.6320 (mmm) REVERT: a 25 TYR cc_start: 0.7643 (m-10) cc_final: 0.6872 (t80) REVERT: b 46 LYS cc_start: 0.8619 (tttm) cc_final: 0.8228 (tttt) REVERT: b 62 MET cc_start: 0.6553 (ptp) cc_final: 0.6318 (pmm) REVERT: b 82 ASN cc_start: 0.7098 (t0) cc_final: 0.6676 (t0) REVERT: b 83 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.4612 (tm) REVERT: d 43 LEU cc_start: 0.8750 (tp) cc_final: 0.8405 (tp) REVERT: d 95 LYS cc_start: 0.9151 (tmmt) cc_final: 0.8531 (ttmt) REVERT: d 111 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: e 3 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8015 (tm) REVERT: e 18 MET cc_start: 0.8225 (mmm) cc_final: 0.7822 (mmm) REVERT: f 24 TYR cc_start: 0.7881 (t80) cc_final: 0.7506 (t80) REVERT: f 30 ASP cc_start: 0.7350 (m-30) cc_final: 0.6915 (m-30) REVERT: f 41 MET cc_start: 0.7752 (ppp) cc_final: 0.6983 (ppp) REVERT: g 23 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7467 (tm-30) REVERT: g 25 GLN cc_start: 0.7029 (tt0) cc_final: 0.6795 (tt0) REVERT: g 85 GLU cc_start: 0.7979 (tt0) cc_final: 0.7627 (tt0) REVERT: g 117 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7520 (tm-30) REVERT: h 15 LEU cc_start: 0.7734 (mm) cc_final: 0.7373 (mt) REVERT: h 114 MET cc_start: 0.8066 (mtt) cc_final: 0.7739 (mtt) REVERT: j 34 PHE cc_start: 0.8687 (t80) cc_final: 0.8461 (t80) REVERT: j 39 ARG cc_start: 0.6680 (tpp80) cc_final: 0.6373 (tpp-160) REVERT: j 43 ASP cc_start: 0.7471 (t0) cc_final: 0.6851 (t0) REVERT: j 45 ASP cc_start: 0.7747 (t0) cc_final: 0.7411 (t0) REVERT: k 53 ASN cc_start: 0.8875 (t0) cc_final: 0.8569 (t0) REVERT: k 58 TYR cc_start: 0.8154 (m-10) cc_final: 0.7941 (m-80) REVERT: l 25 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7369 (tptp) REVERT: l 34 GLU cc_start: 0.7751 (pp20) cc_final: 0.6908 (pm20) REVERT: l 41 MET cc_start: 0.8383 (mmm) cc_final: 0.8136 (mmp) REVERT: l 48 MET cc_start: 0.6972 (mmm) cc_final: 0.5406 (mmm) REVERT: m 34 GLU cc_start: 0.7822 (tt0) cc_final: 0.7336 (mt-10) REVERT: m 84 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6079 (tttt) REVERT: m 112 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: n 61 GLN cc_start: 0.7193 (tp-100) cc_final: 0.6941 (tm-30) REVERT: n 141 GLU cc_start: 0.8273 (pp20) cc_final: 0.7964 (pp20) REVERT: n 149 MET cc_start: 0.6604 (mtm) cc_final: 0.6382 (mtm) REVERT: n 153 LEU cc_start: 0.5230 (mm) cc_final: 0.4955 (mt) REVERT: o 38 MET cc_start: 0.7775 (tpp) cc_final: 0.7391 (mmm) REVERT: o 96 LYS cc_start: 0.8378 (mmtp) cc_final: 0.7941 (mtmt) REVERT: p 7 ASP cc_start: 0.7440 (m-30) cc_final: 0.7165 (m-30) REVERT: p 16 THR cc_start: 0.7438 (p) cc_final: 0.7228 (p) REVERT: p 31 TYR cc_start: 0.7142 (t80) cc_final: 0.6801 (t80) REVERT: q 41 GLU cc_start: 0.7987 (tp30) cc_final: 0.7448 (tp30) REVERT: q 61 TRP cc_start: 0.9179 (p90) cc_final: 0.8758 (p90) REVERT: q 122 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7446 (tm-30) REVERT: r 51 ASN cc_start: 0.7704 (t0) cc_final: 0.7392 (t0) outliers start: 241 outliers final: 160 residues processed: 1552 average time/residue: 0.6082 time to fit residues: 1633.6199 Evaluate side-chains 1498 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1310 time to evaluate : 5.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 136 TYR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 190 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 310 PHE Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 ARG Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 42 PHE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 158 TRP Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 378 LEU Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 286 ILE Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 360 LEU Chi-restraints excluded: chain M residue 361 MET Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 226 TRP Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 50 ASN Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 86 GLU Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 45 CYS Chi-restraints excluded: chain X residue 65 CYS Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain b residue 83 LEU Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 25 LYS Chi-restraints excluded: chain m residue 78 ASN Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 100 GLU Chi-restraints excluded: chain n residue 146 ASP Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 90 GLU Chi-restraints excluded: chain p residue 128 LEU Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 125 VAL Chi-restraints excluded: chain r residue 47 LYS Chi-restraints excluded: chain r residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 464 optimal weight: 0.9990 chunk 748 optimal weight: 2.9990 chunk 456 optimal weight: 4.9990 chunk 355 optimal weight: 9.9990 chunk 520 optimal weight: 10.0000 chunk 785 optimal weight: 10.0000 chunk 722 optimal weight: 10.0000 chunk 625 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 482 optimal weight: 8.9990 chunk 383 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 271 ASN P 131 HIS ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 ASN X 94 GLN X 98 HIS Z 89 ASN b 45 ASN d 46 ASN ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 95 GLN n 11 HIS ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.281 66577 Z= 0.590 Angle : 1.692 51.073 90329 Z= 1.066 Chirality : 0.312 6.409 9974 Planarity : 0.005 0.099 11402 Dihedral : 7.380 178.997 8913 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.51 % Favored : 87.36 % Rotamer: Outliers : 3.28 % Allowed : 24.58 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.09), residues: 7951 helix: -0.41 (0.09), residues: 3750 sheet: -2.25 (0.26), residues: 394 loop : -2.76 (0.10), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 196 HIS 0.020 0.001 HIS n 11 PHE 0.042 0.002 PHE D 171 TYR 0.044 0.002 TYR P 244 ARG 0.015 0.001 ARG B 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15902 Ramachandran restraints generated. 7951 Oldfield, 0 Emsley, 7951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1301 time to evaluate : 5.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8888 (tpp) cc_final: 0.8128 (tpp) REVERT: A 99 SER cc_start: 0.8671 (m) cc_final: 0.7931 (t) REVERT: B 126 MET cc_start: 0.8124 (ttm) cc_final: 0.7867 (ttp) REVERT: B 131 ASN cc_start: 0.8721 (m-40) cc_final: 0.8367 (m110) REVERT: B 172 GLN cc_start: 0.8432 (tt0) cc_final: 0.8192 (tp-100) REVERT: C 39 GLN cc_start: 0.8728 (pp30) cc_final: 0.8459 (pp30) REVERT: C 69 ASN cc_start: 0.8309 (m-40) cc_final: 0.7963 (t0) REVERT: C 77 ASP cc_start: 0.7417 (m-30) cc_final: 0.7195 (m-30) REVERT: C 95 ASN cc_start: 0.9005 (m-40) cc_final: 0.8550 (m-40) REVERT: C 110 TYR cc_start: 0.8540 (p90) cc_final: 0.8234 (p90) REVERT: C 179 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7449 (tp30) REVERT: C 199 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8176 (pp) REVERT: D 23 LYS cc_start: 0.7567 (ptpp) cc_final: 0.6872 (tptp) REVERT: D 35 ASP cc_start: 0.7132 (t70) cc_final: 0.6435 (t0) REVERT: D 72 MET cc_start: 0.7820 (tpp) cc_final: 0.7562 (tpp) REVERT: D 157 HIS cc_start: 0.8240 (t-170) cc_final: 0.7958 (t-170) REVERT: D 189 MET cc_start: 0.7873 (ttt) cc_final: 0.7350 (ttt) REVERT: D 269 LEU cc_start: 0.8175 (mp) cc_final: 0.7962 (mp) REVERT: D 342 MET cc_start: 0.8793 (mmm) cc_final: 0.8332 (tpp) REVERT: D 373 GLU cc_start: 0.7316 (tt0) cc_final: 0.6987 (tt0) REVERT: D 410 MET cc_start: 0.7588 (mtm) cc_final: 0.7225 (mtm) REVERT: E 82 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7421 (mm-30) REVERT: E 101 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: E 122 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7489 (ptt90) REVERT: F 50 LEU cc_start: 0.7936 (mt) cc_final: 0.7120 (tp) REVERT: F 82 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7740 (ppp) REVERT: F 99 GLU cc_start: 0.7180 (mp0) cc_final: 0.6730 (mp0) REVERT: F 137 TYR cc_start: 0.7876 (t80) cc_final: 0.7564 (t80) REVERT: F 272 MET cc_start: 0.9170 (tpt) cc_final: 0.8969 (mmm) REVERT: F 326 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7868 (mm110) REVERT: F 388 GLU cc_start: 0.7658 (mp0) cc_final: 0.7251 (mp0) REVERT: G 107 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8288 (mm) REVERT: G 131 LEU cc_start: 0.8690 (pt) cc_final: 0.7881 (tt) REVERT: G 187 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7899 (pp) REVERT: G 504 ASP cc_start: 0.8236 (m-30) cc_final: 0.7967 (t70) REVERT: G 540 ASP cc_start: 0.7364 (p0) cc_final: 0.6659 (m-30) REVERT: G 556 MET cc_start: 0.8477 (ppp) cc_final: 0.8215 (ppp) REVERT: G 684 MET cc_start: 0.8526 (mmp) cc_final: 0.8128 (mmt) REVERT: H 143 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7860 (mt-10) REVERT: H 172 MET cc_start: 0.8463 (ttp) cc_final: 0.8251 (ttp) REVERT: H 261 MET cc_start: 0.7705 (mmt) cc_final: 0.7377 (mmt) REVERT: H 271 LEU cc_start: 0.8600 (mm) cc_final: 0.8166 (mt) REVERT: I 16 MET cc_start: 0.6314 (tmt) cc_final: 0.5826 (tmt) REVERT: I 22 ASN cc_start: 0.8046 (t0) cc_final: 0.7460 (t0) REVERT: I 25 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7720 (ttm-80) REVERT: I 32 LEU cc_start: 0.8230 (mt) cc_final: 0.7580 (mp) REVERT: I 110 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7988 (ttp80) REVERT: I 144 GLU cc_start: 0.8493 (mp0) cc_final: 0.8267 (mp0) REVERT: I 166 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: J 67 PHE cc_start: 0.8939 (m-80) cc_final: 0.8717 (m-80) REVERT: K 21 MET cc_start: 0.7538 (mmm) cc_final: 0.6944 (ptm) REVERT: K 23 ARG cc_start: 0.6823 (mtp-110) cc_final: 0.5516 (mmt180) REVERT: L 150 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7873 (ttm) REVERT: L 201 ILE cc_start: 0.8975 (mt) cc_final: 0.8452 (mt) REVERT: L 202 MET cc_start: 0.8127 (ptp) cc_final: 0.7897 (ptm) REVERT: L 252 MET cc_start: 0.7828 (tmm) cc_final: 0.7609 (tmm) REVERT: L 261 VAL cc_start: 0.8833 (m) cc_final: 0.8561 (p) REVERT: L 335 PHE cc_start: 0.8287 (m-10) cc_final: 0.8048 (m-80) REVERT: L 352 ASP cc_start: 0.6663 (t70) cc_final: 0.6409 (t0) REVERT: L 383 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6745 (mmm) REVERT: L 421 MET cc_start: 0.8163 (mpp) cc_final: 0.7395 (mpp) REVERT: L 424 MET cc_start: 0.7967 (tmm) cc_final: 0.7369 (tmm) REVERT: L 486 LEU cc_start: 0.8831 (mt) cc_final: 0.8618 (tp) REVERT: L 503 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7568 (mm-30) REVERT: L 587 TYR cc_start: 0.8848 (m-10) cc_final: 0.8216 (m-10) REVERT: M 177 MET cc_start: 0.7793 (ppp) cc_final: 0.7444 (ppp) REVERT: M 216 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8555 (tm) REVERT: M 276 CYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7740 (t) REVERT: M 286 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8059 (mp) REVERT: M 315 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8461 (tm) REVERT: M 329 LEU cc_start: 0.9313 (mm) cc_final: 0.9054 (mp) REVERT: M 355 MET cc_start: 0.8170 (tpp) cc_final: 0.7925 (tpp) REVERT: M 459 MET cc_start: 0.6765 (mmt) cc_final: 0.6556 (mmt) REVERT: N 225 MET cc_start: 0.8314 (mpp) cc_final: 0.8090 (mpp) REVERT: N 282 MET cc_start: 0.7885 (mtp) cc_final: 0.7613 (mtm) REVERT: O 81 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8150 (tmmt) REVERT: O 89 ASN cc_start: 0.6197 (m110) cc_final: 0.5921 (t0) REVERT: O 214 MET cc_start: 0.8088 (tpp) cc_final: 0.7751 (tpp) REVERT: O 271 ASN cc_start: 0.7783 (m110) cc_final: 0.7220 (m110) REVERT: P 57 MET cc_start: 0.8699 (tpp) cc_final: 0.8304 (mmt) REVERT: P 82 ARG cc_start: 0.8455 (tpt-90) cc_final: 0.7847 (tmm160) REVERT: Q 39 VAL cc_start: 0.8991 (t) cc_final: 0.8674 (m) REVERT: Q 82 MET cc_start: 0.8831 (tpt) cc_final: 0.8628 (tpt) REVERT: R 22 ASP cc_start: 0.7523 (m-30) cc_final: 0.7222 (m-30) REVERT: R 57 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7299 (tp) REVERT: R 72 TYR cc_start: 0.8640 (m-80) cc_final: 0.8335 (m-80) REVERT: S 34 ASP cc_start: 0.8552 (m-30) cc_final: 0.7246 (t70) REVERT: S 39 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7377 (ttp-170) REVERT: T 21 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7683 (pp) REVERT: T 71 MET cc_start: 0.5523 (mmm) cc_final: 0.5228 (mmm) REVERT: U 66 ASP cc_start: 0.7783 (m-30) cc_final: 0.7390 (m-30) REVERT: U 74 GLN cc_start: 0.8537 (tp40) cc_final: 0.8090 (tp40) REVERT: V 57 MET cc_start: 0.8730 (ptp) cc_final: 0.8409 (ptp) REVERT: V 81 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7978 (tm) REVERT: V 95 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8270 (pttt) REVERT: W 29 GLU cc_start: 0.7318 (tp30) cc_final: 0.7004 (tp30) REVERT: W 44 GLU cc_start: 0.8365 (tt0) cc_final: 0.7653 (tt0) REVERT: W 96 ILE cc_start: 0.8687 (tt) cc_final: 0.8391 (tp) REVERT: Y 41 SER cc_start: 0.9059 (p) cc_final: 0.8840 (t) REVERT: Y 71 LEU cc_start: 0.8611 (tp) cc_final: 0.8270 (tp) REVERT: Y 125 LYS cc_start: 0.8529 (ttmm) cc_final: 0.7757 (tttm) REVERT: Z 32 TYR cc_start: 0.6248 (m-10) cc_final: 0.5584 (m-10) REVERT: Z 60 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8495 (tt) REVERT: Z 124 TYR cc_start: 0.6840 (p90) cc_final: 0.6451 (p90) REVERT: Z 132 MET cc_start: 0.7865 (tpp) cc_final: 0.7168 (mmm) REVERT: a 1 MET cc_start: 0.6825 (mmm) cc_final: 0.6390 (mmm) REVERT: a 25 TYR cc_start: 0.7660 (m-10) cc_final: 0.6843 (t80) REVERT: a 44 GLN cc_start: 0.8768 (mt0) cc_final: 0.8351 (pt0) REVERT: b 45 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8509 (t0) REVERT: b 46 LYS cc_start: 0.8744 (tttm) cc_final: 0.8483 (tppt) REVERT: b 82 ASN cc_start: 0.7303 (t0) cc_final: 0.6937 (t0) REVERT: b 83 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.5088 (tm) REVERT: d 14 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6615 (tp) REVERT: d 36 LEU cc_start: 0.8376 (mt) cc_final: 0.7798 (tt) REVERT: d 43 LEU cc_start: 0.8897 (tp) cc_final: 0.8556 (tp) REVERT: d 95 LYS cc_start: 0.9182 (tmmt) cc_final: 0.8562 (ttmt) REVERT: d 111 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: e 3 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8092 (tm) REVERT: e 18 MET cc_start: 0.8319 (mmm) cc_final: 0.7792 (mmm) REVERT: e 61 ASP cc_start: 0.8093 (p0) cc_final: 0.7873 (p0) REVERT: f 30 ASP cc_start: 0.7339 (m-30) cc_final: 0.6955 (m-30) REVERT: g 23 GLN cc_start: 0.7590 (tp-100) cc_final: 0.7304 (tm-30) REVERT: g 25 GLN cc_start: 0.7495 (tt0) cc_final: 0.7217 (tt0) REVERT: g 85 GLU cc_start: 0.8035 (tt0) cc_final: 0.7665 (tt0) REVERT: g 117 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7365 (tm-30) REVERT: h 59 TYR cc_start: 0.7860 (t80) cc_final: 0.7603 (t80) REVERT: h 114 MET cc_start: 0.8156 (mtt) cc_final: 0.7818 (mtt) REVERT: j 39 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6746 (tpp80) REVERT: j 43 ASP cc_start: 0.7562 (t0) cc_final: 0.6645 (t0) REVERT: j 45 ASP cc_start: 0.7703 (t0) cc_final: 0.7261 (t0) REVERT: l 34 GLU cc_start: 0.7684 (pp20) cc_final: 0.7067 (pm20) REVERT: l 48 MET cc_start: 0.7350 (mmm) cc_final: 0.7091 (mmm) REVERT: m 34 GLU cc_start: 0.7861 (tt0) cc_final: 0.7414 (mt-10) REVERT: m 84 LYS cc_start: 0.6616 (OUTLIER) cc_final: 0.6014 (tttt) REVERT: m 112 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: n 149 MET cc_start: 0.6707 (mtm) cc_final: 0.6506 (mtm) REVERT: n 153 LEU cc_start: 0.5163 (mm) cc_final: 0.4874 (mt) REVERT: o 96 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8085 (mtmt) REVERT: p 31 TYR cc_start: 0.7062 (t80) cc_final: 0.6663 (t80) REVERT: q 61 TRP cc_start: 0.9186 (p90) cc_final: 0.8357 (p90) REVERT: r 51 ASN cc_start: 0.7754 (t0) cc_final: 0.7541 (t0) REVERT: r 112 LEU cc_start: 0.7328 (tt) cc_final: 0.6750 (mt) outliers start: 230 outliers final: 166 residues processed: 1444 average time/residue: 0.5752 time to fit residues: 1446.4728 Evaluate side-chains 1440 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1248 time to evaluate : 5.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 316 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 362 CYS Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 259 ASN Chi-restraints excluded: chain G residue 279 LEU Chi-restraints excluded: chain G residue 324 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 400 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 614 ASP Chi-restraints excluded: chain G residue 678 SER Chi-restraints excluded: chain H residue 7 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 142 TYR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 159 SER Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 110 ARG Chi-restraints excluded: chain I residue 166 GLU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 130 ILE Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 150 MET Chi-restraints excluded: chain L residue 163 ASP Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 246 LEU Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 338 MET Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain L residue 403 ASN Chi-restraints excluded: chain L residue 431 THR Chi-restraints excluded: chain L residue 526 LEU Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 117 MET Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 234 ILE Chi-restraints excluded: chain M residue 276 CYS Chi-restraints excluded: chain M residue 278 ARG Chi-restraints excluded: chain M residue 281 ASP Chi-restraints excluded: chain M residue 286 ILE Chi-restraints excluded: chain M residue 297 VAL Chi-restraints excluded: chain M residue 315 LEU Chi-restraints excluded: chain M residue 360 LEU Chi-restraints excluded: chain M residue 361 MET Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 410 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 160 THR Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain N residue 249 LEU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 344 ILE Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 81 LYS Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 176 VAL Chi-restraints excluded: chain O residue 226 TRP Chi-restraints excluded: chain O residue 234 VAL Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain P residue 3 HIS Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 64 ASP Chi-restraints excluded: chain P residue 130 ILE Chi-restraints excluded: chain P residue 176 ASP Chi-restraints excluded: chain P residue 231 THR Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain S residue 78 LEU Chi-restraints excluded: chain T residue 21 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 74 GLN Chi-restraints excluded: chain U residue 6 LEU Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain W residue 76 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 65 CYS Chi-restraints excluded: chain X residue 96 PHE Chi-restraints excluded: chain Z residue 60 LEU Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain a residue 9 LEU Chi-restraints excluded: chain a residue 61 TYR Chi-restraints excluded: chain b residue 14 LYS Chi-restraints excluded: chain b residue 34 ILE Chi-restraints excluded: chain b residue 45 ASN Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain b residue 83 LEU Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 82 LEU Chi-restraints excluded: chain d residue 100 ASP Chi-restraints excluded: chain d residue 111 GLU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 63 GLU Chi-restraints excluded: chain e residue 66 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain h residue 136 SER Chi-restraints excluded: chain i residue 4 THR Chi-restraints excluded: chain i residue 27 LEU Chi-restraints excluded: chain i residue 108 THR Chi-restraints excluded: chain j residue 20 SER Chi-restraints excluded: chain k residue 21 LEU Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain l residue 113 PHE Chi-restraints excluded: chain m residue 78 ASN Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain m residue 86 SER Chi-restraints excluded: chain m residue 87 LEU Chi-restraints excluded: chain m residue 112 GLU Chi-restraints excluded: chain n residue 11 HIS Chi-restraints excluded: chain n residue 12 GLN Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 100 GLU Chi-restraints excluded: chain n residue 146 ASP Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 68 CYS Chi-restraints excluded: chain o residue 81 HIS Chi-restraints excluded: chain o residue 90 GLU Chi-restraints excluded: chain p residue 142 TYR Chi-restraints excluded: chain q residue 35 ILE Chi-restraints excluded: chain q residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 496 optimal weight: 9.9990 chunk 665 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 576 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 626 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 642 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 ASN ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 321 HIS ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 ASN ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 77 GLN n 168 HIS ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088204 restraints weight = 170155.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090056 restraints weight = 90558.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091230 restraints weight = 56859.400| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.279 66577 Z= 0.581 Angle : 1.696 51.044 90329 Z= 1.067 Chirality : 0.312 6.413 9974 Planarity : 0.005 0.098 11402 Dihedral : 7.412 179.164 8913 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.45 % Favored : 87.42 % Rotamer: Outliers : 3.39 % Allowed : 24.72 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.09), residues: 7951 helix: -0.44 (0.09), residues: 3741 sheet: -2.26 (0.26), residues: 382 loop : -2.75 (0.10), residues: 3828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 135 HIS 0.028 0.001 HIS n 11 PHE 0.039 0.002 PHE D 171 TYR 0.035 0.002 TYR h 28 ARG 0.016 0.001 ARG B 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22208.15 seconds wall clock time: 387 minutes 30.01 seconds (23250.01 seconds total)