Starting phenix.real_space_refine on Sat Dec 9 18:45:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_4356_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_4356.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_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_4356/12_2023/6g72_4356_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_4356_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_4356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_4356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_4356_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g72_4356/12_2023/6g72_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 25.46, 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: 21.57 Conformation dependent library (CDL) restraints added in 8.3 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: 7.86 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: 16.79 Time building geometry restraints manager: 22.72 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: 2.230 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: 0.040 Extract box with map and model: 12.220 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 142.760 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.080 ------------------------------------------------------------------------------- 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 : 5.575 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 outliers start: 16 outliers final: 3 residues processed: 2513 average time/residue: 0.6588 time to fit residues: 2731.9444 Evaluate side-chains 1371 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1368 time to evaluate : 5.568 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4715 time to fit residues: 10.1549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 665 optimal weight: 0.9990 chunk 597 optimal weight: 7.9990 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: 2.9990 chunk 375 optimal weight: 3.9990 chunk 459 optimal weight: 0.9980 chunk 715 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 48 ASN B 92 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 39 GLN C 67 HIS ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 263 ASN ** 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 H 304 HIS ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 152 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN L 25 ASN L 58 ASN ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 ASN M 366 ASN 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 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** 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 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 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 Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.314 66577 Z= 0.593 Angle : 1.722 51.332 90329 Z= 1.078 Chirality : 0.313 6.630 9974 Planarity : 0.007 0.133 11402 Dihedral : 9.119 172.669 8911 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.99 % Favored : 86.71 % Rotamer: Outliers : 3.45 % Allowed : 15.18 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % 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: -4.31 (0.08), residues: 7951 helix: -2.31 (0.07), residues: 3768 sheet: -3.49 (0.23), residues: 354 loop : -3.41 (0.09), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP V 96 HIS 0.018 0.002 HIS L 230 PHE 0.038 0.002 PHE L 54 TYR 0.032 0.002 TYR C 209 ARG 0.008 0.001 ARG i 19 *********************** 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 1913 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1671 time to evaluate : 5.623 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 outliers start: 242 outliers final: 111 residues processed: 1801 average time/residue: 0.5999 time to fit residues: 1838.3074 Evaluate side-chains 1390 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1279 time to evaluate : 5.567 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 111 outliers final: 1 residues processed: 111 average time/residue: 0.4744 time to fit residues: 106.2610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 397 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 chunk 595 optimal weight: 9.9990 chunk 487 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 716 optimal weight: 5.9990 chunk 774 optimal weight: 7.9990 chunk 638 optimal weight: 10.0000 chunk 710 optimal weight: 0.3980 chunk 244 optimal weight: 4.9990 chunk 575 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 92 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS C 39 GLN D 27 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS ** D 237 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** ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 320 ASN M 48 ASN ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 97 GLN O 287 HIS ** 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 HIS ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN l 27 ASN l 54 GLN 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** ** o 75 ASN ** 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** ** s 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.296 66577 Z= 0.587 Angle : 1.696 51.142 90329 Z= 1.070 Chirality : 0.313 6.555 9974 Planarity : 0.006 0.127 11402 Dihedral : 8.679 174.705 8911 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.21 % Favored : 86.50 % Rotamer: Outliers : 3.39 % Allowed : 17.50 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.23 % 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: -3.59 (0.09), residues: 7951 helix: -1.62 (0.08), residues: 3759 sheet: -3.08 (0.25), residues: 363 loop : -3.15 (0.10), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP V 96 HIS 0.014 0.001 HIS L 230 PHE 0.030 0.002 PHE Y 60 TYR 0.035 0.002 TYR n 114 ARG 0.011 0.001 ARG G 45 *********************** 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 1689 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1451 time to evaluate : 5.702 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 outliers start: 238 outliers final: 101 residues processed: 1593 average time/residue: 0.6434 time to fit residues: 1767.7504 Evaluate side-chains 1342 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1241 time to evaluate : 5.628 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 3 residues processed: 101 average time/residue: 0.5021 time to fit residues: 103.0951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 708 optimal weight: 6.9990 chunk 538 optimal weight: 0.8980 chunk 372 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 481 optimal weight: 10.0000 chunk 719 optimal weight: 4.9990 chunk 761 optimal weight: 10.0000 chunk 375 optimal weight: 0.6980 chunk 681 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- 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 B 104 ASN C 39 GLN C 53 HIS C 160 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 237 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 150 ASN F 24 ASN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** O 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 264 GLN ** P 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 131 HIS ** 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 HIS S 61 GLN T 33 ASN ** 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** i 73 HIS l 54 GLN n 11 HIS ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 138 GLN ** p 27 ASN ** 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** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4854 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= 0.577 Angle : 1.687 51.143 90329 Z= 1.065 Chirality : 0.313 6.467 9974 Planarity : 0.006 0.121 11402 Dihedral : 8.387 178.775 8911 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.09 % Favored : 86.64 % Rotamer: Outliers : 3.47 % Allowed : 19.77 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.17 % 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: -3.20 (0.09), residues: 7951 helix: -1.23 (0.08), residues: 3747 sheet: -2.71 (0.27), residues: 356 loop : -3.04 (0.10), residues: 3848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 413 HIS 0.016 0.001 HIS f 9 PHE 0.026 0.002 PHE Y 60 TYR 0.034 0.002 TYR n 114 ARG 0.010 0.001 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 1660 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1416 time to evaluate : 5.683 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 outliers start: 244 outliers final: 111 residues processed: 1565 average time/residue: 0.6045 time to fit residues: 1640.8321 Evaluate side-chains 1354 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1243 time to evaluate : 5.771 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 3 residues processed: 111 average time/residue: 0.4773 time to fit residues: 108.0867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 634 optimal weight: 2.9990 chunk 432 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 567 optimal weight: 10.0000 chunk 314 optimal weight: 0.7980 chunk 649 optimal weight: 5.9990 chunk 526 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 388 optimal weight: 2.9990 chunk 683 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 C 39 GLN D 27 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** 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 H 258 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 175 ASN M 220 HIS ** M 374 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 323 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 181 HIS 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 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 30 GLN S 61 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN ** l 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 27 ASN ** 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** q 135 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.280 66577 Z= 0.561 Angle : 1.676 51.081 90329 Z= 1.060 Chirality : 0.312 6.448 9974 Planarity : 0.005 0.131 11402 Dihedral : 8.134 178.787 8911 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.69 % Favored : 87.10 % Rotamer: Outliers : 2.63 % Allowed : 21.62 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.17 % 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: -2.98 (0.09), residues: 7951 helix: -1.01 (0.08), residues: 3768 sheet: -2.55 (0.26), residues: 362 loop : -2.99 (0.10), residues: 3821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 487 HIS 0.010 0.001 HIS L 230 PHE 0.029 0.002 PHE Y 60 TYR 0.033 0.002 TYR N 146 ARG 0.012 0.001 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 1578 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1393 time to evaluate : 5.882 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 outliers start: 185 outliers final: 80 residues processed: 1499 average time/residue: 0.5851 time to fit residues: 1545.9673 Evaluate side-chains 1315 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1235 time to evaluate : 5.644 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 2 residues processed: 80 average time/residue: 0.5088 time to fit residues: 83.3458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 256 optimal weight: 0.8980 chunk 685 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 447 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 762 optimal weight: 7.9990 chunk 632 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 252 optimal weight: 2.9990 chunk 400 optimal weight: 0.9980 overall best weight: 1.5942 ------------------------------------------------------------------------------- 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** C 39 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** 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 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN M 44 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 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 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** 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** ** a 27 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 55 HIS ** 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 ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5464 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= 0.553 Angle : 1.669 51.046 90329 Z= 1.057 Chirality : 0.312 6.458 9974 Planarity : 0.005 0.125 11402 Dihedral : 7.783 176.151 8911 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.05 % Favored : 87.72 % Rotamer: Outliers : 2.26 % Allowed : 23.11 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.15 % 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: -2.72 (0.09), residues: 7951 helix: -0.77 (0.08), residues: 3761 sheet: -2.34 (0.27), residues: 361 loop : -2.89 (0.10), residues: 3829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 487 HIS 0.010 0.001 HIS I 67 PHE 0.029 0.002 PHE W 120 TYR 0.041 0.002 TYR C 209 ARG 0.008 0.000 ARG G 45 *********************** 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 1574 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1415 time to evaluate : 5.787 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 outliers start: 159 outliers final: 71 residues processed: 1507 average time/residue: 0.6058 time to fit residues: 1582.7540 Evaluate side-chains 1316 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1245 time to evaluate : 5.688 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 71 outliers final: 1 residues processed: 71 average time/residue: 0.4881 time to fit residues: 72.7123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 735 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 434 optimal weight: 8.9990 chunk 556 optimal weight: 10.0000 chunk 431 optimal weight: 5.9990 chunk 641 optimal weight: 5.9990 chunk 425 optimal weight: 0.9990 chunk 759 optimal weight: 5.9990 chunk 475 optimal weight: 9.9990 chunk 463 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** 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 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS ** F 361 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 ASN I 152 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 83 HIS ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 GLN ** 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** O 294 ASN P 67 GLN ** P 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 321 HIS ** 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** V 52 ASN W 72 ASN X 98 HIS Z 89 ASN a 44 GLN ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 82 HIS l 27 ASN ** l 154 HIS ** 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 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 66 GLN ** 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: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.275 66577 Z= 0.612 Angle : 1.703 51.106 90329 Z= 1.072 Chirality : 0.313 6.573 9974 Planarity : 0.006 0.127 11402 Dihedral : 7.845 175.190 8911 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.42 % Favored : 86.37 % Rotamer: Outliers : 2.48 % Allowed : 23.98 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.20 % 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: -2.75 (0.09), residues: 7951 helix: -0.78 (0.08), residues: 3769 sheet: -2.41 (0.27), residues: 358 loop : -2.92 (0.10), residues: 3824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP M 196 HIS 0.011 0.002 HIS I 67 PHE 0.032 0.002 PHE Y 60 TYR 0.038 0.002 TYR N 146 ARG 0.011 0.001 ARG G 45 *********************** 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 1466 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1292 time to evaluate : 5.691 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 outliers start: 174 outliers final: 93 residues processed: 1395 average time/residue: 0.5931 time to fit residues: 1442.7505 Evaluate side-chains 1285 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1192 time to evaluate : 5.684 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 93 outliers final: 1 residues processed: 93 average time/residue: 0.4854 time to fit residues: 92.7128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 469 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 453 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 chunk 147 optimal weight: 3.9990 chunk 482 optimal weight: 0.0470 chunk 517 optimal weight: 5.9990 chunk 375 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 596 optimal weight: 4.9990 overall best weight: 0.7896 ------------------------------------------------------------------------------- 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 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** ** F 96 ASN ** 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 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 237 ASN ** 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** H 284 GLN I 138 ASN I 152 ASN ** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 400 ASN ** M 374 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 223 ASN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 ASN ** P 3 HIS ** 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 ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 30 GLN X 103 GLN a 27 HIS ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 GLN n 77 GLN ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 60 HIS p 139 GLN ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 66577 Z= 0.549 Angle : 1.680 50.915 90329 Z= 1.059 Chirality : 0.312 6.528 9974 Planarity : 0.005 0.119 11402 Dihedral : 7.612 176.702 8911 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.85 % Favored : 87.98 % Rotamer: Outliers : 1.15 % Allowed : 25.15 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -2.57 (0.09), residues: 7951 helix: -0.62 (0.08), residues: 3788 sheet: -2.33 (0.26), residues: 380 loop : -2.84 (0.10), residues: 3783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP V 96 HIS 0.009 0.001 HIS I 67 PHE 0.029 0.002 PHE Y 60 TYR 0.032 0.002 TYR P 244 ARG 0.006 0.000 ARG G 45 *********************** 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 1476 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1395 time to evaluate : 5.713 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 outliers start: 81 outliers final: 34 residues processed: 1438 average time/residue: 0.6032 time to fit residues: 1504.7772 Evaluate side-chains 1295 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1261 time to evaluate : 5.737 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.5241 time to fit residues: 40.4807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 690 optimal weight: 0.0670 chunk 727 optimal weight: 0.0670 chunk 663 optimal weight: 0.3980 chunk 707 optimal weight: 7.9990 chunk 425 optimal weight: 0.9990 chunk 308 optimal weight: 2.9990 chunk 555 optimal weight: 0.6980 chunk 217 optimal weight: 3.9990 chunk 639 optimal weight: 0.9980 chunk 669 optimal weight: 2.9990 chunk 705 optimal weight: 6.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 34 ASN D 98 GLN ** 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 37 ASN ** E 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 ASN ** 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 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 HIS ** N 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 ASN ** P 3 HIS ** 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 ASN ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 9 HIS ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 154 HIS ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 139 GLN q 72 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 GLN ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.264 66577 Z= 0.550 Angle : 1.684 50.969 90329 Z= 1.060 Chirality : 0.312 6.464 9974 Planarity : 0.005 0.116 11402 Dihedral : 7.415 179.690 8911 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.89 % Favored : 87.95 % Rotamer: Outliers : 1.14 % Allowed : 26.02 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -2.41 (0.09), residues: 7951 helix: -0.50 (0.09), residues: 3756 sheet: -2.20 (0.27), residues: 380 loop : -2.75 (0.10), residues: 3815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP M 196 HIS 0.017 0.001 HIS f 9 PHE 0.031 0.001 PHE L 466 TYR 0.037 0.002 TYR P 244 ARG 0.008 0.000 ARG G 45 *********************** 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 1464 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1384 time to evaluate : 5.785 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 outliers start: 80 outliers final: 40 residues processed: 1428 average time/residue: 0.6121 time to fit residues: 1510.8734 Evaluate side-chains 1296 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1256 time to evaluate : 5.771 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5054 time to fit residues: 45.6690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 355 optimal weight: 5.9990 chunk 520 optimal weight: 8.9990 chunk 785 optimal weight: 9.9990 chunk 722 optimal weight: 8.9990 chunk 625 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 482 optimal weight: 0.0570 chunk 383 optimal weight: 5.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- 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 71 HIS C 39 GLN ** 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 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 ASN ** 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 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 425 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 ASN ** P 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 234 ASN ** Q 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 95 GLN ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 GLN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.261 66577 Z= 0.558 Angle : 1.692 50.975 90329 Z= 1.063 Chirality : 0.312 6.459 9974 Planarity : 0.005 0.114 11402 Dihedral : 7.355 176.691 8911 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.73 % Favored : 88.13 % Rotamer: Outliers : 0.51 % Allowed : 26.67 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -2.38 (0.09), residues: 7951 helix: -0.45 (0.09), residues: 3753 sheet: -2.17 (0.27), residues: 392 loop : -2.75 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 169 HIS 0.011 0.001 HIS L 248 PHE 0.036 0.002 PHE J 50 TYR 0.033 0.002 TYR n 114 ARG 0.016 0.000 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 1352 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1316 time to evaluate : 5.820 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 outliers start: 36 outliers final: 20 residues processed: 1331 average time/residue: 0.6249 time to fit residues: 1450.7622 Evaluate side-chains 1277 residues out of total 7074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1257 time to evaluate : 5.636 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5173 time to fit residues: 26.8735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 788 random chunks: chunk 496 optimal weight: 10.0000 chunk 665 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 576 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 626 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 642 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 172 GLN ** 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 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 250 ASN ** 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 43 HIS ** G 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 374 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** ** O 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 180 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** Q 50 ASN R 13 HIS ** R 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN ** n 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 72 ASN ** q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 20 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090642 restraints weight = 168746.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092573 restraints weight = 88492.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093852 restraints weight = 54849.025| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.261 66577 Z= 0.559 Angle : 1.692 50.999 90329 Z= 1.063 Chirality : 0.312 6.457 9974 Planarity : 0.005 0.114 11402 Dihedral : 7.301 174.722 8911 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.22 % Favored : 87.65 % Rotamer: Outliers : 0.57 % Allowed : 26.97 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -2.33 (0.09), residues: 7951 helix: -0.41 (0.09), residues: 3778 sheet: -2.13 (0.27), residues: 384 loop : -2.74 (0.10), residues: 3789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP M 196 HIS 0.009 0.001 HIS D 398 PHE 0.032 0.002 PHE J 50 TYR 0.049 0.002 TYR P 244 ARG 0.015 0.000 ARG B 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22106.82 seconds wall clock time: 386 minutes 12.57 seconds (23172.57 seconds total)