Starting phenix.real_space_refine on Fri Feb 16 10:02:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkq_11258/02_2024/6zkq_11258_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.017 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 44 5.49 5 S 466 5.16 5 C 43597 2.51 5 N 11138 2.21 5 O 12078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "9 PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67353 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "A" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2489 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} 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: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} 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: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} 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: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} 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: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" 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: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "6" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'3PE': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 205 Unusual residues: {'3PE': 1, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 157 Unusual residues: {'3PE': 2, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "n" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "o" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 90 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 26 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 103.364 53.831 240.658 1.00 18.54 S ATOM 2676 SG CYS 1 359 110.578 54.011 241.331 1.00 35.77 S ATOM 4116 SG CYS 2 103 101.664 49.529 259.844 1.00 77.22 S ATOM 4150 SG CYS 2 108 99.302 47.190 262.090 1.00 73.82 S ATOM 4430 SG CYS 2 144 102.921 45.972 256.367 1.00 67.33 S ATOM 4453 SG CYS 2 148 101.173 43.186 257.991 1.00 73.53 S ATOM 5793 SG CYS 3 114 105.669 71.894 225.690 1.00 54.23 S ATOM 5732 SG CYS 3 105 100.560 75.418 227.588 1.00 29.13 S ATOM 5753 SG CYS 3 108 106.682 77.154 229.107 1.00 55.93 S ATOM 6125 SG CYS 3 156 112.844 64.481 230.346 1.00 68.38 S ATOM 6102 SG CYS 3 153 110.876 67.619 235.847 1.00 21.41 S ATOM 6149 SG CYS 3 159 116.948 68.359 234.032 1.00 55.43 S ATOM 6479 SG CYS 3 203 112.924 70.750 230.293 1.00 72.63 S ATOM 5238 SG CYS 3 41 112.118 57.948 228.434 1.00 40.07 S ATOM 5324 SG CYS 3 52 108.361 58.960 227.984 1.00 53.32 S ATOM 5349 SG CYS 3 55 108.577 54.048 224.397 1.00 20.52 S ATOM 5450 SG CYS 3 69 112.363 54.097 225.692 1.00 24.10 S ATOM 16341 SG CYS 6 149 87.102 95.182 207.955 1.00 63.29 S ATOM 15607 SG CYS 6 54 83.606 94.877 202.173 1.00 75.13 S ATOM 17533 SG CYS 9 116 91.513 96.157 214.310 1.00 37.42 S ATOM 17580 SG CYS 9 122 92.023 91.924 219.165 1.00 20.32 S ATOM 17307 SG CYS 9 87 96.000 91.425 213.921 1.00 41.70 S ATOM 17609 SG CYS 9 126 94.420 88.519 226.507 1.00 22.75 S ATOM 17280 SG CYS 9 83 97.836 90.177 221.292 1.00 22.28 S ATOM 17238 SG CYS 9 77 100.219 91.911 226.961 1.00 48.79 S ATOM 17257 SG CYS 9 80 99.288 85.367 225.416 1.00 35.17 S ATOM 41151 SG CYS b 59 96.161 84.513 241.790 1.00 37.05 S ATOM 41329 SG CYS b 84 99.317 84.123 239.689 1.00 31.75 S ATOM 41351 SG CYS b 87 97.465 87.146 240.434 1.00 37.49 S Time building chain proxies: 27.26, per 1000 atoms: 0.40 Number of scatterers: 67353 At special positions: 0 Unit cell: (176.79, 198.37, 291.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 466 16.00 P 44 15.00 O 12078 8.00 N 11138 7.00 C 43597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.04 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.89 Conformation dependent library (CDL) restraints added in 11.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 500 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb=" SF4 3 802 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 201 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 403 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 328 helices and 29 sheets defined 50.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.50 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' Processing helix chain '1' and resid 33 through 39 removed outlier: 3.611A pdb=" N SER 1 38 " --> pdb=" O LYS 1 34 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG 1 39 " --> pdb=" O GLY 1 35 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 63 removed outlier: 3.853A pdb=" N LYS 1 51 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY 1 52 " --> pdb=" O ILE 1 48 " (cutoff:3.500A) Proline residue: 1 53 - end of helix removed outlier: 3.708A pdb=" N ILE 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 81 removed outlier: 3.668A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 107 through 113 Processing helix chain '1' and resid 115 through 128 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.216A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 388 through 399 Processing helix chain '1' and resid 407 through 436 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.879A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.766A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 72 Processing helix chain '2' and resid 77 through 86 removed outlier: 4.579A pdb=" N GLU 2 82 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 177 Processing helix chain '3' and resid 26 through 33 removed outlier: 3.755A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 150 through 152 No H-bonds generated for 'chain '3' and resid 150 through 152' Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 202 Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 296 through 308 removed outlier: 4.043A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 312 through 314 No H-bonds generated for 'chain '3' and resid 312 through 314' Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 359 through 361 No H-bonds generated for 'chain '3' and resid 359 through 361' Processing helix chain '3' and resid 369 through 372 removed outlier: 3.747A pdb=" N GLU 3 372 " --> pdb=" O ALA 3 369 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 369 through 372' Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 433 removed outlier: 4.101A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.537A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 505 Processing helix chain '3' and resid 511 through 515 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 649 Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' Processing helix chain '3' and resid 678 through 680 No H-bonds generated for 'chain '3' and resid 678 through 680' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.611A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' Processing helix chain '4' and resid 87 through 93 removed outlier: 4.212A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 99 No H-bonds generated for 'chain '4' and resid 96 through 99' Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 removed outlier: 3.570A pdb=" N ILE 4 161 " --> pdb=" O HIS 4 157 " (cutoff:3.500A) Processing helix chain '4' and resid 165 through 184 removed outlier: 4.106A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 4.047A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 238 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 258 through 263 removed outlier: 4.397A pdb=" N SER 4 263 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 315 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 352 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.589A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 removed outlier: 4.115A pdb=" N VAL 4 415 " --> pdb=" O LEU 4 411 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA 4 416 " --> pdb=" O ALA 4 412 " (cutoff:3.500A) Processing helix chain '4' and resid 425 through 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 57 through 66 Processing helix chain '5' and resid 125 through 138 removed outlier: 3.611A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE 5 138 " --> pdb=" O TRP 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 44 removed outlier: 3.807A pdb=" N SER 6 44 " --> pdb=" O ALA 6 40 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 106 Processing helix chain '6' and resid 117 through 122 Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 41 Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 122 through 125 No H-bonds generated for 'chain '9' and resid 122 through 125' Processing helix chain '9' and resid 144 through 147 Processing helix chain '9' and resid 151 through 172 removed outlier: 5.701A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.772A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix removed outlier: 3.690A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 55 Processing helix chain 'H' and resid 68 through 84 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 3.814A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 154 removed outlier: 3.921A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 217 through 242 Processing helix chain 'H' and resid 252 through 273 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 5.335A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.657A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 75 removed outlier: 4.377A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET J 74 " --> pdb=" O TYR J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.087A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 3 through 19 removed outlier: 3.749A pdb=" N ASN K 7 " --> pdb=" O LEU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 50 Processing helix chain 'K' and resid 54 through 85 removed outlier: 3.841A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.556A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR K 85 " --> pdb=" O SER K 82 " (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 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.790A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 55 removed outlier: 3.917A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 110 Proline residue: L 91 - end of helix removed outlier: 3.877A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS L 109 " --> pdb=" O MET L 105 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER L 110 " --> pdb=" O TRP L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 133 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.988A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 232 through 238 removed outlier: 3.850A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.264A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.666A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.271A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (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 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.180A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 469 removed outlier: 3.826A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (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 509 removed outlier: 4.099A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 removed outlier: 4.010A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.780A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG L 535 " --> pdb=" O ILE L 532 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.276A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN L 546 " --> pdb=" O THR L 543 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 599 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.097A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.633A pdb=" N THR M 27 " --> pdb=" O ILE M 23 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 81 removed outlier: 3.792A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 3.608A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 109 removed outlier: 3.622A pdb=" N MET M 108 " --> pdb=" O LEU M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 136 removed outlier: 4.587A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.779A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN M 144 " --> pdb=" O GLU M 141 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE M 149 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU M 154 " --> pdb=" O PHE M 151 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU M 158 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 4.406A pdb=" N MET M 171 " --> pdb=" O GLN M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.870A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 222 removed outlier: 4.395A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 248 removed outlier: 4.642A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.123A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 removed outlier: 4.317A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.305A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 351 No H-bonds generated for 'chain 'M' and resid 348 through 351' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.896A pdb=" N ILE M 393 " --> pdb=" O ASN M 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET M 396 " --> pdb=" O ILE M 393 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY M 397 " --> pdb=" O ILE M 394 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU M 398 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER M 407 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR M 414 " --> pdb=" O LEU M 411 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.177A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 112 through 121 Proline residue: N 116 - end of helix removed outlier: 3.544A pdb=" N THR N 119 " --> pdb=" O PRO N 116 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY N 121 " --> pdb=" O VAL N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.063A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 168 Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.222A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 3.591A pdb=" N GLY N 252 " --> pdb=" O LEU N 248 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 271 removed outlier: 4.709A pdb=" N LYS N 263 " --> pdb=" O GLY N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.628A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.802A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 332 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.720A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 8 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 79 Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.809A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 63 through 66 removed outlier: 3.976A pdb=" N TYR W 66 " --> pdb=" O HIS W 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 63 through 66' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 21 removed outlier: 3.774A pdb=" N LEU X 21 " --> pdb=" O TYR X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 74 removed outlier: 3.800A pdb=" N LEU Y 67 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.671A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 3.633A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 42 through 44 No H-bonds generated for 'chain 'a' and resid 42 through 44' Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.729A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.785A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 43 No H-bonds generated for 'chain 'b' and resid 40 through 43' Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 29 No H-bonds generated for 'chain 'c' and resid 27 through 29' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 118 through 122 Processing helix chain 'd' and resid 30 through 41 removed outlier: 3.790A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 59 removed outlier: 4.581A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 85 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 182 No H-bonds generated for 'chain 'd' and resid 179 through 182' Processing helix chain 'd' and resid 207 through 218 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 300 through 302 No H-bonds generated for 'chain 'd' and resid 300 through 302' Processing helix chain 'd' and resid 310 through 321 removed outlier: 5.005A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 39 removed outlier: 3.649A pdb=" N LYS e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.266A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 3.917A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.481A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.741A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.032A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 73 through 82 Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 35 through 46 removed outlier: 3.874A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL k 42 " --> pdb=" O ALA k 39 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS k 45 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU k 46 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.207A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 217 removed outlier: 5.394A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix removed outlier: 5.088A pdb=" N GLU k 216 " --> pdb=" O PRO k 212 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS k 217 " --> pdb=" O GLU k 213 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 246 through 248 No H-bonds generated for 'chain 'k' and resid 246 through 248' Processing helix chain 'k' and resid 253 through 264 removed outlier: 3.526A pdb=" N GLN k 264 " --> pdb=" O ARG k 260 " (cutoff:3.500A) Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 272 through 274 No H-bonds generated for 'chain 'k' and resid 272 through 274' Processing helix chain 'k' and resid 286 through 298 removed outlier: 3.724A pdb=" N GLU k 298 " --> pdb=" O GLN k 294 " (cutoff:3.500A) Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 47 through 54 removed outlier: 4.058A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 87 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 16 through 34 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 47 removed outlier: 3.793A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 63 through 66 No H-bonds generated for 'chain 'n' and resid 63 through 66' Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.661A pdb=" N ARG o 19 " --> pdb=" O ASP o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 95 removed outlier: 3.736A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 22 Processing helix chain 'p' and resid 26 through 50 removed outlier: 3.884A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.593A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 78 No H-bonds generated for 'chain 'p' and resid 76 through 78' Processing helix chain 'p' and resid 83 through 92 Processing helix chain 'p' and resid 95 through 115 Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 136 Processing helix chain 'r' and resid 5 through 24 Processing helix chain 'r' and resid 68 through 87 removed outlier: 5.384A pdb=" N ILE r 76 " --> pdb=" O THR r 72 " (cutoff:3.500A) Proline residue: r 77 - end of helix Processing helix chain 's' and resid 2 through 7 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 48 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 92 through 95 removed outlier: 4.246A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 92 through 95' Processing helix chain 't' and resid 100 through 103 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 139 removed outlier: 3.928A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 4.106A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS w 98 " --> pdb=" O ARG w 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG w 100 " --> pdb=" O VAL w 97 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU w 101 " --> pdb=" O LYS w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 15 through 33 Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 31 Proline residue: z 19 - end of helix removed outlier: 3.616A pdb=" N ASN z 31 " --> pdb=" O HIS z 27 " (cutoff:3.500A) Processing helix chain 'z' and resid 42 through 54 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 5.870A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 253 through 258 Processing sheet with id= C, first strand: chain '1' and resid 306 through 308 removed outlier: 7.034A pdb=" N MET 1 337 " --> pdb=" O LEU 1 295 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL 1 297 " --> pdb=" O ILE 1 335 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE 1 335 " --> pdb=" O VAL 1 297 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 137 through 142 removed outlier: 6.721A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN 2 159 " --> pdb=" O ILE 2 156 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 9 through 13 Processing sheet with id= F, first strand: chain '3' and resid 146 through 148 Processing sheet with id= G, first strand: chain '3' and resid 173 through 175 Processing sheet with id= H, first strand: chain '3' and resid 223 through 228 removed outlier: 3.530A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 283 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.733A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 405 through 409 Processing sheet with id= L, first strand: chain '3' and resid 571 through 574 removed outlier: 3.695A pdb=" N ALA 3 571 " --> pdb=" O THR 3 583 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 47 through 51 removed outlier: 6.323A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 361 through 369 Processing sheet with id= O, first strand: chain '5' and resid 74 through 79 removed outlier: 6.690A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE 5 105 " --> pdb=" O LEU 5 96 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 172 through 177 Processing sheet with id= Q, first strand: chain '6' and resid 47 through 51 removed outlier: 6.559A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 65 through 67 Processing sheet with id= S, first strand: chain '9' and resid 92 through 98 removed outlier: 5.564A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 3.658A pdb=" N ASN L 65 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= Y, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= Z, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.737A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL d 90 " --> pdb=" O VAL d 20 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'e' and resid 51 through 56 removed outlier: 3.679A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'i' and resid 60 through 63 removed outlier: 3.600A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.665A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC 2769 hydrogen bonds defined for protein. 7815 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: 22.66 Time building geometry restraints manager: 24.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.43: 28355 1.43 - 1.66: 39803 1.66 - 1.89: 758 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 68996 Sorted by residual: bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.00e-02 1.00e+04 4.04e+01 bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.593 0.240 3.80e-02 6.93e+02 3.98e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.329 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" OB3 CDL z 101 " pdb=" PB2 CDL z 101 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.00e-02 1.00e+04 3.51e+01 bond pdb=" CA PRO 4 359 " pdb=" C PRO 4 359 " ideal model delta sigma weight residual 1.514 1.547 -0.033 5.50e-03 3.31e+04 3.50e+01 ... (remaining 68991 not shown) Histogram of bond angle deviations from ideal: 62.31 - 77.87: 72 77.87 - 93.43: 8 93.43 - 108.99: 6919 108.99 - 124.54: 84546 124.54 - 140.10: 1687 Bond angle restraints: 93232 Sorted by residual: angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 89.92 14.41 1.14e+00 7.69e-01 1.60e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 89.89 14.44 1.20e+00 6.94e-01 1.45e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 91.58 12.75 1.14e+00 7.69e-01 1.25e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 129.23 -21.49 1.95e+00 2.62e-01 1.21e+02 angle pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " pdb="FE2 FES 3 803 " ideal model delta sigma weight residual 75.66 88.04 -12.38 1.14e+00 7.69e-01 1.18e+02 ... (remaining 93227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 41187 34.15 - 68.30: 723 68.30 - 102.46: 47 102.46 - 136.61: 2 136.61 - 170.76: 5 Dihedral angle restraints: 41964 sinusoidal: 18204 harmonic: 23760 Sorted by residual: dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual -180.00 -130.46 -49.54 0 5.00e+00 4.00e-02 9.82e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual -180.00 -137.45 -42.55 0 5.00e+00 4.00e-02 7.24e+01 dihedral pdb=" C10 FMN 1 501 " pdb=" C1' FMN 1 501 " pdb=" N10 FMN 1 501 " pdb=" C2' FMN 1 501 " ideal model delta sinusoidal sigma weight residual 257.59 86.83 170.76 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.217: 10072 4.217 - 8.433: 5 8.433 - 12.650: 0 12.650 - 16.866: 0 16.866 - 21.083: 24 Chirality restraints: 10101 Sorted by residual: chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.53 21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 9 402 " pdb=" S1 SF4 9 402 " pdb=" S2 SF4 9 402 " pdb=" S3 SF4 9 402 " 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="FE4 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S3 SF4 3 801 " both_signs ideal model delta sigma weight residual False 10.55 -10.52 21.08 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10098 not shown) Planarity restraints: 11630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B NDP d 401 " -0.071 2.00e-02 2.50e+03 3.00e-02 2.48e+01 pdb=" C2A NDP d 401 " 0.010 2.00e-02 2.50e+03 pdb=" C4A NDP d 401 " 0.025 2.00e-02 2.50e+03 pdb=" C5A NDP d 401 " 0.013 2.00e-02 2.50e+03 pdb=" C6A NDP d 401 " -0.003 2.00e-02 2.50e+03 pdb=" C8A NDP d 401 " 0.023 2.00e-02 2.50e+03 pdb=" N1A NDP d 401 " -0.007 2.00e-02 2.50e+03 pdb=" N3A NDP d 401 " 0.023 2.00e-02 2.50e+03 pdb=" N6A NDP d 401 " -0.047 2.00e-02 2.50e+03 pdb=" N7A NDP d 401 " 0.020 2.00e-02 2.50e+03 pdb=" N9A NDP d 401 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.032 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP A 106 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.012 2.00e-02 2.50e+03 2.77e-02 1.54e+01 pdb=" CG TYR 9 40 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 11627 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 17420 2.80 - 3.38: 71862 3.38 - 3.97: 135688 3.97 - 4.55: 193295 4.55 - 5.14: 285832 Nonbonded interactions: 704097 Sorted by model distance: nonbonded pdb=" O ILE L 556 " pdb=" OG1 THR L 560 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU 4 224 " pdb=" OH TYR 9 40 " model vdw 2.248 2.440 nonbonded pdb=" O VAL 5 183 " pdb=" OG1 THR g 100 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR s 8 " pdb=" O PRO v 123 " model vdw 2.260 2.440 ... (remaining 704092 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 'X' and resid 5 through 86) selection = chain 'j' } 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 individual isotropic 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: 0.970 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: 0.080 Extract box with map and model: 6.880 Check model and map are aligned: 0.760 Set scattering table: 0.490 Process input model: 168.620 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.270 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.009 0.240 68996 Z= 0.606 Angle : 1.030 21.487 93232 Z= 0.549 Chirality : 1.025 21.083 10101 Planarity : 0.008 0.069 11630 Dihedral : 12.453 170.762 26619 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.27 % Favored : 95.72 % Rotamer: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.17 (0.07), residues: 8036 helix: -2.03 (0.06), residues: 4249 sheet: -1.95 (0.22), residues: 427 loop : -2.04 (0.09), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP A 106 HIS 0.018 0.003 HIS Z 55 PHE 0.055 0.004 PHE J 17 TYR 0.064 0.003 TYR 6 125 ARG 0.026 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2029 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2025 time to evaluate : 5.912 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: 1 77 LEU cc_start: 0.9237 (tp) cc_final: 0.9031 (mt) REVERT: 1 249 ARG cc_start: 0.7706 (mpp-170) cc_final: 0.7473 (mtm-85) REVERT: 1 313 GLU cc_start: 0.8502 (tp30) cc_final: 0.8240 (mt-10) REVERT: 1 356 HIS cc_start: 0.7893 (m-70) cc_final: 0.7679 (m-70) REVERT: 1 357 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8046 (mm-30) REVERT: 1 431 GLN cc_start: 0.8313 (pt0) cc_final: 0.7949 (tt0) REVERT: 1 436 GLN cc_start: 0.7826 (pt0) cc_final: 0.7618 (mt0) REVERT: 2 40 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7883 (mt-10) REVERT: 2 112 ASN cc_start: 0.8709 (t0) cc_final: 0.8426 (t0) REVERT: 2 114 ASP cc_start: 0.8746 (m-30) cc_final: 0.8544 (m-30) REVERT: 2 127 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8265 (mtpp) REVERT: 3 71 MET cc_start: 0.9159 (tpp) cc_final: 0.8669 (tpp) REVERT: 3 287 GLU cc_start: 0.8149 (pm20) cc_final: 0.7890 (mp0) REVERT: 3 306 MET cc_start: 0.8609 (tpt) cc_final: 0.8341 (tpp) REVERT: 3 418 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7879 (ttp80) REVERT: 3 475 GLN cc_start: 0.7494 (mm110) cc_final: 0.6955 (mp10) REVERT: 3 643 GLN cc_start: 0.7523 (tp40) cc_final: 0.7086 (tp40) REVERT: 4 62 LEU cc_start: 0.8619 (tp) cc_final: 0.8414 (tp) REVERT: 4 182 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8892 (tm-30) REVERT: 4 213 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8380 (mm-30) REVERT: 5 10 THR cc_start: 0.9062 (p) cc_final: 0.8801 (t) REVERT: 5 14 ARG cc_start: 0.8317 (ttt90) cc_final: 0.8057 (ttm-80) REVERT: 5 147 ASP cc_start: 0.7782 (t0) cc_final: 0.7054 (p0) REVERT: 5 158 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8484 (mp0) REVERT: 6 48 MET cc_start: 0.8784 (tmt) cc_final: 0.8032 (tmt) REVERT: 6 70 ASP cc_start: 0.9042 (t70) cc_final: 0.8828 (t0) REVERT: 6 106 GLN cc_start: 0.8232 (mt0) cc_final: 0.7992 (mm110) REVERT: 9 78 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.8790 (pp) REVERT: 9 151 LYS cc_start: 0.9162 (tttt) cc_final: 0.8947 (tttp) REVERT: A 23 TRP cc_start: 0.6737 (m100) cc_final: 0.6535 (m100) REVERT: A 108 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7903 (tm-30) REVERT: H 163 SER cc_start: 0.9269 (m) cc_final: 0.8984 (p) REVERT: H 263 SER cc_start: 0.9002 (m) cc_final: 0.8791 (m) REVERT: J 99 MET cc_start: 0.5997 (mmt) cc_final: 0.5636 (mtp) REVERT: K 16 LEU cc_start: 0.8751 (tp) cc_final: 0.8530 (tp) REVERT: K 22 TYR cc_start: 0.8169 (m-10) cc_final: 0.7757 (m-10) REVERT: L 306 THR cc_start: 0.8890 (t) cc_final: 0.8671 (m) REVERT: L 407 TRP cc_start: 0.8452 (t-100) cc_final: 0.8080 (t-100) REVERT: L 540 MET cc_start: 0.8308 (mtm) cc_final: 0.7340 (mmt) REVERT: L 544 MET cc_start: 0.6743 (tmm) cc_final: 0.6463 (mmt) REVERT: L 547 LYS cc_start: 0.7882 (mttm) cc_final: 0.6959 (tmmt) REVERT: L 571 MET cc_start: 0.6996 (ttm) cc_final: 0.6699 (mtp) REVERT: L 581 LYS cc_start: 0.6815 (mtmm) cc_final: 0.6530 (mttt) REVERT: M 19 LYS cc_start: 0.8329 (mttp) cc_final: 0.8024 (mtpp) REVERT: M 231 LEU cc_start: 0.8624 (mt) cc_final: 0.8416 (mt) REVERT: N 11 MET cc_start: 0.8488 (mmp) cc_final: 0.8126 (mtp) REVERT: N 151 LEU cc_start: 0.8586 (tp) cc_final: 0.8212 (tp) REVERT: N 181 TYR cc_start: 0.8940 (m-80) cc_final: 0.8655 (m-80) REVERT: N 269 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8535 (mm-30) REVERT: V 126 MET cc_start: 0.7741 (mtt) cc_final: 0.7505 (mtt) REVERT: X 68 GLU cc_start: 0.6536 (pt0) cc_final: 0.6052 (tp30) REVERT: X 84 LYS cc_start: 0.8720 (mmtp) cc_final: 0.8434 (mmtm) REVERT: Y 11 ASP cc_start: 0.8665 (m-30) cc_final: 0.8271 (m-30) REVERT: Y 64 GLN cc_start: 0.8461 (tt0) cc_final: 0.8010 (mt0) REVERT: Y 82 THR cc_start: 0.8512 (m) cc_final: 0.7980 (p) REVERT: Z 5 ASP cc_start: 0.8587 (t0) cc_final: 0.8284 (t0) REVERT: a 58 LEU cc_start: 0.8882 (mt) cc_final: 0.8662 (mt) REVERT: a 72 SER cc_start: 0.9005 (p) cc_final: 0.8706 (m) REVERT: b 34 GLU cc_start: 0.8851 (tt0) cc_final: 0.8542 (tp30) REVERT: c 18 ASP cc_start: 0.8738 (t70) cc_final: 0.8508 (t70) REVERT: c 112 LYS cc_start: 0.8802 (pttt) cc_final: 0.8455 (ptmt) REVERT: d 79 ASP cc_start: 0.8025 (t0) cc_final: 0.7434 (m-30) REVERT: d 115 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8220 (tp40) REVERT: d 140 LYS cc_start: 0.8376 (mtmm) cc_final: 0.7559 (pptt) REVERT: d 290 THR cc_start: 0.8694 (t) cc_final: 0.8468 (m) REVERT: e 19 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8414 (mtm-85) REVERT: e 39 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7754 (mtp-110) REVERT: e 74 LYS cc_start: 0.8374 (mttp) cc_final: 0.8053 (mmtt) REVERT: f 32 ASP cc_start: 0.8923 (t0) cc_final: 0.8673 (t0) REVERT: g 56 LYS cc_start: 0.9008 (tmmt) cc_final: 0.8517 (tttp) REVERT: h 17 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.7891 (mtt90) REVERT: i 1 MET cc_start: 0.7230 (tpt) cc_final: 0.6988 (ttp) REVERT: i 7 LEU cc_start: 0.9026 (mt) cc_final: 0.8563 (mp) REVERT: i 32 ASP cc_start: 0.8540 (t70) cc_final: 0.8301 (t0) REVERT: i 43 LYS cc_start: 0.8767 (ptmm) cc_final: 0.8518 (ptmm) REVERT: i 71 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8651 (tttp) REVERT: i 128 SER cc_start: 0.9202 (t) cc_final: 0.8932 (p) REVERT: i 132 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8374 (tttt) REVERT: i 135 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8251 (mt0) REVERT: j 24 LYS cc_start: 0.8104 (ttmp) cc_final: 0.7816 (tptp) REVERT: j 29 LYS cc_start: 0.7560 (tttp) cc_final: 0.6902 (ttpp) REVERT: j 39 ASP cc_start: 0.7345 (m-30) cc_final: 0.6988 (t0) REVERT: j 54 MET cc_start: 0.7656 (mmt) cc_final: 0.7437 (mmt) REVERT: j 78 ASP cc_start: 0.8070 (m-30) cc_final: 0.7791 (m-30) REVERT: j 82 ASP cc_start: 0.7235 (m-30) cc_final: 0.6640 (p0) REVERT: k 16 LYS cc_start: 0.8276 (mttt) cc_final: 0.7928 (mmtt) REVERT: k 94 TYR cc_start: 0.8446 (t80) cc_final: 0.7832 (t80) REVERT: k 135 LEU cc_start: 0.8936 (tp) cc_final: 0.8674 (tt) REVERT: k 161 CYS cc_start: 0.9429 (p) cc_final: 0.8973 (p) REVERT: k 255 LYS cc_start: 0.8651 (mttt) cc_final: 0.8337 (mttp) REVERT: l 84 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8245 (ttmm) REVERT: m 14 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7775 (mptt) REVERT: m 71 ASP cc_start: 0.7670 (m-30) cc_final: 0.7247 (m-30) REVERT: n 30 THR cc_start: 0.8166 (m) cc_final: 0.7824 (p) REVERT: n 85 TYR cc_start: 0.4850 (t80) cc_final: 0.4613 (t80) REVERT: q 55 GLU cc_start: 0.8942 (tp30) cc_final: 0.8691 (tp30) REVERT: q 120 MET cc_start: 0.8560 (tpp) cc_final: 0.8250 (tpt) REVERT: r 8 LYS cc_start: 0.8340 (mtpt) cc_final: 0.7823 (tppt) REVERT: r 107 ASP cc_start: 0.6386 (m-30) cc_final: 0.6052 (p0) REVERT: t 71 TRP cc_start: 0.7713 (t-100) cc_final: 0.7490 (t-100) REVERT: t 93 TYR cc_start: 0.8652 (m-80) cc_final: 0.8437 (m-80) REVERT: t 100 GLU cc_start: 0.7057 (pp20) cc_final: 0.6839 (pm20) REVERT: w 54 ASP cc_start: 0.8915 (t70) cc_final: 0.8462 (t0) REVERT: w 98 LYS cc_start: 0.8023 (tmtp) cc_final: 0.7710 (tmtt) REVERT: y 28 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7349 (mtm180) REVERT: y 49 LYS cc_start: 0.7096 (mtmt) cc_final: 0.6896 (mttp) REVERT: z 35 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8654 (mt-10) outliers start: 4 outliers final: 2 residues processed: 2029 average time/residue: 0.7321 time to fit residues: 2448.8655 Evaluate side-chains 1302 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1299 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain L residue 599 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 8.9990 chunk 602 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 406 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 623 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 378 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 chunk 721 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 356 HIS 1 373 ASN 1 437 HIS 2 101 GLN 2 121 GLN 3 179 ASN ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 459 GLN ** 4 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 6 82 GLN 9 65 HIS A 2 ASN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS K 7 ASN L 210 ASN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 270 ASN L 434 GLN L 446 ASN L 509 HIS ** L 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN M 138 ASN M 279 GLN M 333 ASN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN N 273 ASN W 44 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 GLN Y 72 GLN Z 90 GLN Z 106 GLN Z 114 GLN a 40 ASN b 36 ASN b 51 GLN b 95 HIS d 87 HIS f 49 GLN f 72 GLN g 94 ASN g 125 HIS i 69 ASN k 92 ASN k 153 ASN k 200 GLN k 271 ASN o 59 HIS r 25 GLN s 3 HIS t 12 GLN t 25 HIS t 32 HIS t 72 HIS t 77 GLN t 138 GLN u 6 HIS v 132 GLN w 41 ASN w 57 ASN y 30 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.271 68996 Z= 0.545 Angle : 1.580 51.337 93232 Z= 1.020 Chirality : 0.310 6.500 10101 Planarity : 0.005 0.060 11630 Dihedral : 12.667 170.131 10498 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.87 % Allowed : 8.39 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.33 (0.09), residues: 8036 helix: -0.31 (0.07), residues: 4228 sheet: -1.63 (0.23), residues: 424 loop : -1.41 (0.10), residues: 3384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP w 26 HIS 0.007 0.001 HIS Z 55 PHE 0.035 0.002 PHE N 292 TYR 0.029 0.002 TYR L 422 ARG 0.009 0.001 ARG o 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1431 time to evaluate : 5.973 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: 1 82 MET cc_start: 0.9021 (mmm) cc_final: 0.8476 (mtp) REVERT: 1 249 ARG cc_start: 0.7907 (mpp-170) cc_final: 0.7546 (mtm-85) REVERT: 1 431 GLN cc_start: 0.8113 (pt0) cc_final: 0.7702 (tt0) REVERT: 2 112 ASN cc_start: 0.8771 (t0) cc_final: 0.8471 (t0) REVERT: 2 114 ASP cc_start: 0.8735 (m-30) cc_final: 0.8516 (m-30) REVERT: 2 127 LYS cc_start: 0.8549 (ptpt) cc_final: 0.8297 (mtpp) REVERT: 3 287 GLU cc_start: 0.8145 (pm20) cc_final: 0.7839 (mp0) REVERT: 3 306 MET cc_start: 0.8594 (tpt) cc_final: 0.8296 (tpp) REVERT: 3 418 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7805 (ttp80) REVERT: 3 475 GLN cc_start: 0.7255 (mm110) cc_final: 0.6873 (mp10) REVERT: 5 10 THR cc_start: 0.9070 (p) cc_final: 0.8861 (t) REVERT: 5 65 ARG cc_start: 0.9159 (tmm-80) cc_final: 0.8749 (tmm160) REVERT: 5 147 ASP cc_start: 0.7670 (t0) cc_final: 0.6956 (p0) REVERT: 5 158 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8409 (mp0) REVERT: 6 48 MET cc_start: 0.8853 (tmt) cc_final: 0.8003 (tmt) REVERT: 6 70 ASP cc_start: 0.9058 (t70) cc_final: 0.8793 (t0) REVERT: 6 106 GLN cc_start: 0.8225 (mt0) cc_final: 0.7986 (mm110) REVERT: 9 78 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8759 (pp) REVERT: 9 151 LYS cc_start: 0.9166 (tttt) cc_final: 0.8913 (tttp) REVERT: A 23 TRP cc_start: 0.6716 (m100) cc_final: 0.6487 (m100) REVERT: A 108 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8008 (tm-30) REVERT: J 99 MET cc_start: 0.6008 (mmt) cc_final: 0.5576 (mtp) REVERT: J 118 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7151 (mppt) REVERT: K 22 TYR cc_start: 0.8186 (m-10) cc_final: 0.7807 (m-10) REVERT: L 61 MET cc_start: 0.8496 (ptp) cc_final: 0.8290 (ptp) REVERT: L 314 MET cc_start: 0.9071 (tpt) cc_final: 0.8856 (tpt) REVERT: L 540 MET cc_start: 0.8061 (mtm) cc_final: 0.7079 (mmt) REVERT: L 544 MET cc_start: 0.6833 (tmm) cc_final: 0.6364 (mmt) REVERT: L 547 LYS cc_start: 0.7805 (mttm) cc_final: 0.6963 (tmmt) REVERT: L 561 ILE cc_start: 0.7471 (pt) cc_final: 0.7248 (pt) REVERT: M 36 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9039 (tp) REVERT: M 114 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8228 (tt0) REVERT: M 207 MET cc_start: 0.8746 (tpp) cc_final: 0.8496 (mmt) REVERT: M 343 ILE cc_start: 0.9023 (tp) cc_final: 0.8817 (tt) REVERT: M 398 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8213 (mt) REVERT: N 11 MET cc_start: 0.8558 (mmp) cc_final: 0.8006 (mtp) REVERT: N 151 LEU cc_start: 0.8660 (tp) cc_final: 0.8280 (tp) REVERT: N 181 TYR cc_start: 0.8922 (m-80) cc_final: 0.8549 (m-80) REVERT: N 269 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8497 (mm-30) REVERT: V 90 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5782 (tt) REVERT: V 126 MET cc_start: 0.7701 (mtt) cc_final: 0.7482 (mtt) REVERT: W 109 GLU cc_start: 0.8609 (tp30) cc_final: 0.8234 (mm-30) REVERT: X 68 GLU cc_start: 0.6525 (pt0) cc_final: 0.6017 (tp30) REVERT: Y 64 GLN cc_start: 0.8409 (tt0) cc_final: 0.8050 (mt0) REVERT: Y 82 THR cc_start: 0.8650 (m) cc_final: 0.8116 (p) REVERT: Y 141 TYR cc_start: 0.9241 (m-80) cc_final: 0.8996 (m-80) REVERT: Z 5 ASP cc_start: 0.8510 (t0) cc_final: 0.8263 (t0) REVERT: a 72 SER cc_start: 0.8946 (p) cc_final: 0.8662 (m) REVERT: b 4 THR cc_start: 0.8523 (m) cc_final: 0.8284 (m) REVERT: b 34 GLU cc_start: 0.8719 (tt0) cc_final: 0.8445 (tp30) REVERT: c 112 LYS cc_start: 0.8730 (pttt) cc_final: 0.8431 (ptmt) REVERT: d 140 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7594 (pptt) REVERT: d 290 THR cc_start: 0.8769 (t) cc_final: 0.8551 (m) REVERT: e 39 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7823 (mtp-110) REVERT: e 74 LYS cc_start: 0.8225 (mttp) cc_final: 0.7904 (mmtt) REVERT: f 32 ASP cc_start: 0.8949 (t0) cc_final: 0.8677 (t0) REVERT: i 7 LEU cc_start: 0.8915 (mt) cc_final: 0.8477 (mp) REVERT: i 32 ASP cc_start: 0.8561 (t70) cc_final: 0.8219 (t0) REVERT: i 135 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8258 (mt0) REVERT: j 20 LYS cc_start: 0.8174 (tmmt) cc_final: 0.7940 (mttt) REVERT: j 29 LYS cc_start: 0.7658 (tttp) cc_final: 0.6929 (ttpp) REVERT: j 39 ASP cc_start: 0.7286 (m-30) cc_final: 0.7055 (t0) REVERT: j 78 ASP cc_start: 0.8052 (m-30) cc_final: 0.7790 (m-30) REVERT: j 82 ASP cc_start: 0.7293 (m-30) cc_final: 0.6720 (p0) REVERT: k 16 LYS cc_start: 0.8241 (mttt) cc_final: 0.7921 (mmtt) REVERT: k 94 TYR cc_start: 0.8428 (t80) cc_final: 0.7909 (t80) REVERT: k 134 PHE cc_start: 0.8950 (m-80) cc_final: 0.8669 (m-80) REVERT: k 135 LEU cc_start: 0.8952 (tp) cc_final: 0.8716 (tt) REVERT: k 173 ASP cc_start: 0.6794 (m-30) cc_final: 0.5845 (t0) REVERT: l 4 ASP cc_start: 0.8688 (t70) cc_final: 0.8442 (t70) REVERT: l 87 LYS cc_start: 0.6661 (mmtt) cc_final: 0.5880 (mmmt) REVERT: m 14 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7787 (mptt) REVERT: m 30 ILE cc_start: 0.8836 (pp) cc_final: 0.8431 (mt) REVERT: m 71 ASP cc_start: 0.7701 (m-30) cc_final: 0.7240 (m-30) REVERT: n 22 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7202 (mmtp) REVERT: n 85 TYR cc_start: 0.4711 (t80) cc_final: 0.4481 (t80) REVERT: q 84 GLN cc_start: 0.8894 (tp40) cc_final: 0.8601 (tt0) REVERT: r 8 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7784 (tppt) REVERT: r 27 LEU cc_start: 0.8025 (mm) cc_final: 0.7771 (mt) REVERT: r 98 GLU cc_start: 0.8157 (tt0) cc_final: 0.7948 (mt-10) REVERT: r 107 ASP cc_start: 0.6529 (m-30) cc_final: 0.6148 (p0) REVERT: s 87 ASP cc_start: 0.7623 (m-30) cc_final: 0.7368 (m-30) REVERT: v 152 PRO cc_start: 0.6214 (Cg_exo) cc_final: 0.5851 (Cg_endo) REVERT: v 157 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7241 (mm-30) REVERT: w 26 TRP cc_start: 0.7178 (p90) cc_final: 0.6943 (p90) REVERT: w 49 LYS cc_start: 0.8243 (ptpp) cc_final: 0.8023 (mtmm) REVERT: w 54 ASP cc_start: 0.8935 (t70) cc_final: 0.8421 (t0) REVERT: w 98 LYS cc_start: 0.8059 (tmtp) cc_final: 0.7804 (tmtt) REVERT: y 24 TYR cc_start: 0.8165 (t80) cc_final: 0.7840 (t80) REVERT: y 28 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7224 (mtm180) REVERT: y 49 LYS cc_start: 0.7121 (mtmt) cc_final: 0.6871 (mttp) outliers start: 133 outliers final: 83 residues processed: 1507 average time/residue: 0.6665 time to fit residues: 1695.0730 Evaluate side-chains 1346 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1258 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 368 ILE Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 54 LEU Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain p residue 103 VAL Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain u residue 37 LEU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 600 optimal weight: 9.9990 chunk 491 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 723 optimal weight: 30.0000 chunk 781 optimal weight: 20.0000 chunk 644 optimal weight: 5.9990 chunk 717 optimal weight: 10.0000 chunk 246 optimal weight: 2.9990 chunk 580 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 402 HIS ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 546 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 82 GLN A 2 ASN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS J 175 ASN K 52 HIS K 83 ASN ** 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 479 GLN L 509 HIS L 524 ASN M 138 ASN M 333 ASN M 399 ASN ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN e 92 ASN k 97 GLN k 271 ASN k 287 HIS t 12 GLN t 72 HIS t 77 GLN ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 68996 Z= 0.571 Angle : 1.578 50.624 93232 Z= 1.018 Chirality : 0.311 6.427 10101 Planarity : 0.005 0.059 11630 Dihedral : 12.133 171.265 10496 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.37 % Allowed : 10.52 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.62 (0.09), residues: 8036 helix: 0.28 (0.08), residues: 4240 sheet: -1.47 (0.24), residues: 409 loop : -1.07 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 144 HIS 0.010 0.001 HIS 1 356 PHE 0.033 0.002 PHE N 292 TYR 0.028 0.002 TYR L 422 ARG 0.007 0.001 ARG L 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1291 time to evaluate : 5.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 82 MET cc_start: 0.9061 (mmm) cc_final: 0.8724 (mtp) REVERT: 1 249 ARG cc_start: 0.7899 (mpp-170) cc_final: 0.7535 (mtm-85) REVERT: 1 431 GLN cc_start: 0.8068 (pt0) cc_final: 0.7743 (tt0) REVERT: 2 112 ASN cc_start: 0.8758 (t0) cc_final: 0.8417 (t0) REVERT: 2 114 ASP cc_start: 0.8748 (m-30) cc_final: 0.8533 (m-30) REVERT: 2 127 LYS cc_start: 0.8599 (ptpt) cc_final: 0.8350 (mtpp) REVERT: 3 71 MET cc_start: 0.9201 (tpp) cc_final: 0.8996 (tpt) REVERT: 3 287 GLU cc_start: 0.8196 (pm20) cc_final: 0.7903 (mp0) REVERT: 3 306 MET cc_start: 0.8573 (tpt) cc_final: 0.8292 (tpp) REVERT: 3 418 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7805 (ttp80) REVERT: 3 475 GLN cc_start: 0.7277 (mm110) cc_final: 0.6683 (mp10) REVERT: 5 10 THR cc_start: 0.9066 (p) cc_final: 0.8824 (t) REVERT: 5 147 ASP cc_start: 0.7812 (t0) cc_final: 0.7028 (p0) REVERT: 6 48 MET cc_start: 0.8911 (tmt) cc_final: 0.8101 (tmt) REVERT: 6 70 ASP cc_start: 0.9137 (t70) cc_final: 0.8883 (t0) REVERT: 6 106 GLN cc_start: 0.8293 (mt0) cc_final: 0.8039 (mm110) REVERT: 9 78 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8809 (pp) REVERT: 9 151 LYS cc_start: 0.9206 (tttt) cc_final: 0.8954 (tttp) REVERT: A 23 TRP cc_start: 0.6716 (m100) cc_final: 0.6502 (m100) REVERT: A 108 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7965 (tm-30) REVERT: H 163 SER cc_start: 0.9179 (m) cc_final: 0.8867 (p) REVERT: J 99 MET cc_start: 0.6072 (mmt) cc_final: 0.5542 (mtp) REVERT: J 118 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7210 (mppt) REVERT: K 22 TYR cc_start: 0.8243 (m-10) cc_final: 0.7876 (m-10) REVERT: L 314 MET cc_start: 0.9044 (tpt) cc_final: 0.8832 (tpt) REVERT: L 425 ARG cc_start: 0.8006 (ttt180) cc_final: 0.7784 (ttt180) REVERT: L 540 MET cc_start: 0.7958 (mtm) cc_final: 0.6898 (mmt) REVERT: L 544 MET cc_start: 0.6938 (tmm) cc_final: 0.6405 (mmt) REVERT: L 547 LYS cc_start: 0.7846 (mttm) cc_final: 0.6982 (tmmt) REVERT: L 561 ILE cc_start: 0.7319 (pt) cc_final: 0.7060 (pt) REVERT: M 36 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9007 (tt) REVERT: M 114 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: M 207 MET cc_start: 0.8633 (tpp) cc_final: 0.8299 (mmt) REVERT: M 350 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8151 (t) REVERT: N 11 MET cc_start: 0.8563 (mmp) cc_final: 0.8016 (mtp) REVERT: N 151 LEU cc_start: 0.8786 (tp) cc_final: 0.8436 (tp) REVERT: N 269 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8530 (mm-30) REVERT: V 7 GLN cc_start: 0.6366 (pt0) cc_final: 0.5942 (mt0) REVERT: V 90 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5846 (tt) REVERT: X 68 GLU cc_start: 0.6585 (pt0) cc_final: 0.5962 (tp30) REVERT: Y 64 GLN cc_start: 0.8386 (tt0) cc_final: 0.8057 (mt0) REVERT: Y 141 TYR cc_start: 0.9239 (m-80) cc_final: 0.8972 (m-80) REVERT: Z 5 ASP cc_start: 0.8546 (t0) cc_final: 0.8290 (t0) REVERT: a 72 SER cc_start: 0.9060 (p) cc_final: 0.8752 (m) REVERT: b 34 GLU cc_start: 0.8730 (tt0) cc_final: 0.8451 (tp30) REVERT: c 36 ARG cc_start: 0.8634 (ttt-90) cc_final: 0.8415 (ttt-90) REVERT: c 112 LYS cc_start: 0.8740 (pttt) cc_final: 0.8414 (ptmt) REVERT: d 140 LYS cc_start: 0.8451 (mtmm) cc_final: 0.7624 (pptt) REVERT: d 290 THR cc_start: 0.8807 (t) cc_final: 0.8602 (m) REVERT: e 39 ARG cc_start: 0.8432 (mtt180) cc_final: 0.7795 (mtp-110) REVERT: e 74 LYS cc_start: 0.8208 (mttp) cc_final: 0.7863 (mmtt) REVERT: f 32 ASP cc_start: 0.8995 (t0) cc_final: 0.8743 (t0) REVERT: i 7 LEU cc_start: 0.8903 (mt) cc_final: 0.8442 (mp) REVERT: i 9 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7806 (mtm180) REVERT: i 32 ASP cc_start: 0.8654 (t70) cc_final: 0.8307 (t0) REVERT: i 135 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8217 (mt0) REVERT: j 20 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7939 (mttt) REVERT: j 29 LYS cc_start: 0.7678 (tttp) cc_final: 0.7030 (ttpp) REVERT: j 39 ASP cc_start: 0.7333 (m-30) cc_final: 0.7087 (t0) REVERT: j 78 ASP cc_start: 0.8097 (m-30) cc_final: 0.7775 (m-30) REVERT: j 82 ASP cc_start: 0.7349 (m-30) cc_final: 0.6734 (p0) REVERT: k 16 LYS cc_start: 0.8249 (mttt) cc_final: 0.7960 (mmtt) REVERT: k 94 TYR cc_start: 0.8601 (t80) cc_final: 0.8024 (t80) REVERT: k 134 PHE cc_start: 0.9028 (m-80) cc_final: 0.8786 (m-80) REVERT: k 135 LEU cc_start: 0.9031 (tp) cc_final: 0.8790 (tt) REVERT: k 173 ASP cc_start: 0.6904 (m-30) cc_final: 0.5817 (t0) REVERT: k 185 LYS cc_start: 0.7454 (mtmp) cc_final: 0.7063 (tppt) REVERT: k 255 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8309 (mttp) REVERT: l 4 ASP cc_start: 0.8754 (t0) cc_final: 0.8503 (t70) REVERT: l 87 LYS cc_start: 0.6737 (mmtt) cc_final: 0.5862 (mmmt) REVERT: m 14 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7734 (mptt) REVERT: m 30 ILE cc_start: 0.8856 (pp) cc_final: 0.8468 (mt) REVERT: m 71 ASP cc_start: 0.7664 (m-30) cc_final: 0.7179 (m-30) REVERT: n 22 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7547 (mmmt) REVERT: p 65 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (mp) REVERT: r 8 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7764 (tppt) REVERT: t 56 MET cc_start: 0.7762 (ppp) cc_final: 0.7073 (mtp) REVERT: v 8 MET cc_start: 0.7046 (ttp) cc_final: 0.6802 (tmm) REVERT: v 152 PRO cc_start: 0.6419 (Cg_exo) cc_final: 0.6134 (Cg_endo) REVERT: w 49 LYS cc_start: 0.8294 (ptpp) cc_final: 0.8077 (mtmm) REVERT: w 54 ASP cc_start: 0.8954 (t70) cc_final: 0.8389 (t0) REVERT: w 98 LYS cc_start: 0.7983 (tmtp) cc_final: 0.7764 (tmtt) REVERT: y 24 TYR cc_start: 0.8153 (t80) cc_final: 0.7827 (t80) REVERT: y 28 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7208 (mtm180) REVERT: y 49 LYS cc_start: 0.7143 (mtmt) cc_final: 0.6836 (mttp) outliers start: 169 outliers final: 122 residues processed: 1388 average time/residue: 0.6518 time to fit residues: 1530.0961 Evaluate side-chains 1325 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1197 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 442 VAL Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 253 GLU Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 458 LEU Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 554 ASP Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 73 ILE Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 64 ASP Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain u residue 37 LEU Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 4.9990 chunk 543 optimal weight: 3.9990 chunk 375 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 345 optimal weight: 20.0000 chunk 485 optimal weight: 10.0000 chunk 725 optimal weight: 10.0000 chunk 768 optimal weight: 6.9990 chunk 379 optimal weight: 0.9990 chunk 687 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 GLN ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 409 HIS ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** L 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 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** M 138 ASN M 399 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 ASN k 271 ASN q 53 ASN t 72 HIS u 13 GLN ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 68996 Z= 0.536 Angle : 1.560 50.588 93232 Z= 1.011 Chirality : 0.310 6.382 10101 Planarity : 0.004 0.056 11630 Dihedral : 11.641 171.093 10496 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.36 % Allowed : 11.61 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.15 (0.09), residues: 8036 helix: 0.67 (0.08), residues: 4231 sheet: -1.17 (0.25), residues: 394 loop : -0.86 (0.11), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 144 HIS 0.006 0.001 HIS u 50 PHE 0.038 0.001 PHE v 111 TYR 0.028 0.001 TYR r 94 ARG 0.007 0.000 ARG i 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1292 time to evaluate : 5.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 82 MET cc_start: 0.9069 (mmm) cc_final: 0.8797 (mtp) REVERT: 1 249 ARG cc_start: 0.7900 (mpp-170) cc_final: 0.7525 (mtm-85) REVERT: 1 431 GLN cc_start: 0.8056 (pt0) cc_final: 0.7737 (tt0) REVERT: 2 112 ASN cc_start: 0.8744 (t0) cc_final: 0.8420 (t0) REVERT: 2 114 ASP cc_start: 0.8734 (m-30) cc_final: 0.8528 (m-30) REVERT: 2 127 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8348 (mtpp) REVERT: 3 306 MET cc_start: 0.8557 (tpt) cc_final: 0.8273 (tpp) REVERT: 3 418 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7774 (ttp80) REVERT: 3 475 GLN cc_start: 0.7210 (mm110) cc_final: 0.6584 (mp10) REVERT: 4 62 LEU cc_start: 0.8689 (tp) cc_final: 0.8007 (pt) REVERT: 4 82 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8573 (mp) REVERT: 5 10 THR cc_start: 0.9061 (p) cc_final: 0.8828 (t) REVERT: 5 147 ASP cc_start: 0.7805 (t0) cc_final: 0.7050 (p0) REVERT: 5 178 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7834 (t0) REVERT: 6 48 MET cc_start: 0.8915 (tmt) cc_final: 0.8078 (tmt) REVERT: 6 70 ASP cc_start: 0.9114 (t70) cc_final: 0.8846 (t0) REVERT: 6 102 LYS cc_start: 0.9083 (tttt) cc_final: 0.8789 (tttp) REVERT: 6 106 GLN cc_start: 0.8290 (mt0) cc_final: 0.8055 (mm110) REVERT: 9 78 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8782 (pp) REVERT: 9 151 LYS cc_start: 0.9197 (tttt) cc_final: 0.8970 (tttp) REVERT: A 23 TRP cc_start: 0.6657 (m100) cc_final: 0.6446 (m100) REVERT: A 108 GLN cc_start: 0.8705 (mm-40) cc_final: 0.7946 (tm-30) REVERT: J 99 MET cc_start: 0.5977 (mmt) cc_final: 0.5519 (mtp) REVERT: J 118 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7202 (mppt) REVERT: K 22 TYR cc_start: 0.8252 (m-10) cc_final: 0.7915 (m-10) REVERT: L 425 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7700 (ttt180) REVERT: L 540 MET cc_start: 0.7738 (mtm) cc_final: 0.6813 (mmt) REVERT: L 544 MET cc_start: 0.6953 (tmm) cc_final: 0.6430 (mmt) REVERT: L 547 LYS cc_start: 0.7841 (mttm) cc_final: 0.7001 (tmmt) REVERT: L 561 ILE cc_start: 0.7118 (pt) cc_final: 0.6883 (pt) REVERT: M 36 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9016 (tt) REVERT: M 350 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8133 (t) REVERT: N 11 MET cc_start: 0.8530 (mmp) cc_final: 0.7947 (mtp) REVERT: N 151 LEU cc_start: 0.8778 (tp) cc_final: 0.8441 (tp) REVERT: N 269 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8544 (mm-30) REVERT: V 7 GLN cc_start: 0.6320 (pt0) cc_final: 0.5849 (mt0) REVERT: V 90 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5716 (tt) REVERT: V 126 MET cc_start: 0.7428 (mtt) cc_final: 0.6783 (mtt) REVERT: W 102 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: W 109 GLU cc_start: 0.8611 (tp30) cc_final: 0.8161 (mm-30) REVERT: X 68 GLU cc_start: 0.6593 (pt0) cc_final: 0.5927 (tp30) REVERT: Y 64 GLN cc_start: 0.8382 (tt0) cc_final: 0.8109 (mt0) REVERT: Y 79 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: Y 141 TYR cc_start: 0.9218 (m-80) cc_final: 0.8926 (m-80) REVERT: Z 5 ASP cc_start: 0.8511 (t0) cc_final: 0.8264 (t0) REVERT: a 72 SER cc_start: 0.9036 (p) cc_final: 0.8766 (m) REVERT: b 34 GLU cc_start: 0.8728 (tt0) cc_final: 0.8430 (tp30) REVERT: c 36 ARG cc_start: 0.8601 (ttt-90) cc_final: 0.8312 (ttt90) REVERT: c 112 LYS cc_start: 0.8738 (pttt) cc_final: 0.8418 (ptmt) REVERT: d 140 LYS cc_start: 0.8525 (mtmm) cc_final: 0.7609 (pptt) REVERT: d 290 THR cc_start: 0.8788 (t) cc_final: 0.8577 (m) REVERT: e 39 ARG cc_start: 0.8425 (mtt180) cc_final: 0.7857 (mtp-110) REVERT: e 74 LYS cc_start: 0.8166 (mttp) cc_final: 0.7841 (mmtt) REVERT: f 32 ASP cc_start: 0.8963 (t0) cc_final: 0.8703 (t0) REVERT: f 70 GLN cc_start: 0.8705 (pt0) cc_final: 0.8359 (pt0) REVERT: h 8 GLN cc_start: 0.9194 (tt0) cc_final: 0.8949 (mt0) REVERT: i 7 LEU cc_start: 0.8909 (mt) cc_final: 0.8429 (mp) REVERT: i 32 ASP cc_start: 0.8606 (t70) cc_final: 0.8276 (t0) REVERT: i 135 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8207 (mt0) REVERT: j 20 LYS cc_start: 0.8130 (tmmt) cc_final: 0.7889 (mttt) REVERT: j 29 LYS cc_start: 0.7670 (tttp) cc_final: 0.7081 (ttpp) REVERT: j 34 SER cc_start: 0.7619 (t) cc_final: 0.7294 (t) REVERT: j 39 ASP cc_start: 0.7311 (m-30) cc_final: 0.7040 (t0) REVERT: j 78 ASP cc_start: 0.8093 (m-30) cc_final: 0.7759 (m-30) REVERT: j 82 ASP cc_start: 0.7306 (m-30) cc_final: 0.6735 (p0) REVERT: k 16 LYS cc_start: 0.8201 (mttt) cc_final: 0.7883 (mmtt) REVERT: k 94 TYR cc_start: 0.8594 (t80) cc_final: 0.8095 (t80) REVERT: k 134 PHE cc_start: 0.8994 (m-80) cc_final: 0.8766 (m-80) REVERT: k 135 LEU cc_start: 0.8998 (tp) cc_final: 0.8790 (tt) REVERT: k 173 ASP cc_start: 0.6825 (m-30) cc_final: 0.5771 (t0) REVERT: k 185 LYS cc_start: 0.7466 (mtmp) cc_final: 0.7106 (tppt) REVERT: l 4 ASP cc_start: 0.8770 (t0) cc_final: 0.8535 (t70) REVERT: l 87 LYS cc_start: 0.6624 (mmtt) cc_final: 0.5798 (mmmt) REVERT: m 14 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7661 (mmtm) REVERT: m 30 ILE cc_start: 0.8816 (pp) cc_final: 0.8480 (mt) REVERT: m 71 ASP cc_start: 0.7679 (m-30) cc_final: 0.7196 (m-30) REVERT: n 22 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7482 (mmmt) REVERT: p 65 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (mp) REVERT: r 8 LYS cc_start: 0.8312 (mtpt) cc_final: 0.7752 (tppt) REVERT: r 98 GLU cc_start: 0.8341 (tt0) cc_final: 0.7997 (mt-10) REVERT: v 8 MET cc_start: 0.7090 (ttp) cc_final: 0.6815 (tmm) REVERT: v 152 PRO cc_start: 0.6534 (Cg_exo) cc_final: 0.6284 (Cg_endo) REVERT: w 49 LYS cc_start: 0.8291 (ptpp) cc_final: 0.8055 (mtmm) REVERT: w 54 ASP cc_start: 0.8855 (t70) cc_final: 0.8341 (t0) REVERT: w 98 LYS cc_start: 0.7972 (tmtp) cc_final: 0.7740 (tmtt) REVERT: y 24 TYR cc_start: 0.8029 (t80) cc_final: 0.7760 (t80) REVERT: y 28 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7201 (mtm180) REVERT: y 49 LYS cc_start: 0.7011 (mtmt) cc_final: 0.6710 (mttp) outliers start: 168 outliers final: 113 residues processed: 1388 average time/residue: 0.6595 time to fit residues: 1546.3886 Evaluate side-chains 1343 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1221 time to evaluate : 5.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 265 ASP Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 82 LEU Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 6 residue 60 MET Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 103 SER Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 350 THR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 282 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain q residue 135 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 7.9990 chunk 436 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 572 optimal weight: 0.0980 chunk 317 optimal weight: 5.9990 chunk 655 optimal weight: 9.9990 chunk 531 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 392 optimal weight: 9.9990 chunk 689 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 55 GLN 4 79 HIS ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 21 GLN 6 82 GLN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS L 135 ASN L 175 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN M 399 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 GLN g 94 ASN k 271 ASN l 26 HIS l 97 HIS t 72 HIS t 77 GLN t 138 GLN y 30 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 68996 Z= 0.582 Angle : 1.577 50.680 93232 Z= 1.018 Chirality : 0.310 6.391 10101 Planarity : 0.004 0.060 11630 Dihedral : 11.490 171.706 10496 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.88 % Allowed : 12.10 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.00 (0.09), residues: 8036 helix: 0.76 (0.08), residues: 4223 sheet: -1.12 (0.25), residues: 404 loop : -0.74 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 144 HIS 0.008 0.001 HIS u 50 PHE 0.032 0.002 PHE v 111 TYR 0.029 0.002 TYR d 145 ARG 0.009 0.001 ARG q 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1264 time to evaluate : 6.024 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: 1 82 MET cc_start: 0.9089 (mmm) cc_final: 0.8725 (mtp) REVERT: 1 249 ARG cc_start: 0.7907 (mpp-170) cc_final: 0.7515 (mtm-85) REVERT: 1 425 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8164 (tt0) REVERT: 1 431 GLN cc_start: 0.8074 (pt0) cc_final: 0.7750 (tt0) REVERT: 2 112 ASN cc_start: 0.8727 (t0) cc_final: 0.8379 (t0) REVERT: 2 114 ASP cc_start: 0.8759 (m-30) cc_final: 0.8552 (m-30) REVERT: 2 127 LYS cc_start: 0.8666 (ptpt) cc_final: 0.8407 (mtpp) REVERT: 3 31 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8035 (mp0) REVERT: 3 71 MET cc_start: 0.9196 (tpp) cc_final: 0.8981 (tpt) REVERT: 3 306 MET cc_start: 0.8588 (tpt) cc_final: 0.8295 (tpp) REVERT: 3 418 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7823 (ttp80) REVERT: 3 475 GLN cc_start: 0.7187 (mm110) cc_final: 0.6602 (mp10) REVERT: 4 82 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8677 (mp) REVERT: 4 275 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7940 (p90) REVERT: 5 147 ASP cc_start: 0.7944 (t0) cc_final: 0.7137 (p0) REVERT: 6 70 ASP cc_start: 0.9126 (t70) cc_final: 0.8792 (t0) REVERT: 6 102 LYS cc_start: 0.9074 (tttt) cc_final: 0.8786 (tttp) REVERT: 6 106 GLN cc_start: 0.8346 (mt0) cc_final: 0.8088 (mm110) REVERT: 9 78 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8828 (pp) REVERT: 9 151 LYS cc_start: 0.9221 (tttt) cc_final: 0.8978 (tttp) REVERT: A 23 TRP cc_start: 0.6671 (m100) cc_final: 0.6471 (m100) REVERT: A 108 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8111 (tm-30) REVERT: J 99 MET cc_start: 0.5994 (mmt) cc_final: 0.5574 (mtp) REVERT: J 118 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7164 (mppt) REVERT: K 22 TYR cc_start: 0.8313 (m-10) cc_final: 0.8008 (m-10) REVERT: L 488 MET cc_start: 0.7937 (mmm) cc_final: 0.7196 (ptt) REVERT: L 525 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7584 (mm) REVERT: L 540 MET cc_start: 0.7821 (mtm) cc_final: 0.6787 (mmt) REVERT: L 544 MET cc_start: 0.7009 (tmm) cc_final: 0.6443 (mmt) REVERT: L 547 LYS cc_start: 0.7933 (mttm) cc_final: 0.7093 (tmmt) REVERT: L 561 ILE cc_start: 0.7070 (pt) cc_final: 0.6869 (pt) REVERT: L 601 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7046 (tt) REVERT: M 36 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9058 (tt) REVERT: N 11 MET cc_start: 0.8528 (mmp) cc_final: 0.7934 (mtp) REVERT: N 151 LEU cc_start: 0.8836 (tp) cc_final: 0.8520 (tp) REVERT: V 7 GLN cc_start: 0.6253 (pt0) cc_final: 0.5759 (mt0) REVERT: V 90 LEU cc_start: 0.6178 (OUTLIER) cc_final: 0.5821 (tt) REVERT: W 102 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: X 68 GLU cc_start: 0.6464 (pt0) cc_final: 0.5822 (tp30) REVERT: Y 64 GLN cc_start: 0.8386 (tt0) cc_final: 0.8101 (mt0) REVERT: Y 141 TYR cc_start: 0.9240 (m-80) cc_final: 0.8988 (m-80) REVERT: Z 5 ASP cc_start: 0.8575 (t0) cc_final: 0.8300 (t0) REVERT: a 72 SER cc_start: 0.9112 (p) cc_final: 0.8804 (m) REVERT: b 34 GLU cc_start: 0.8729 (tt0) cc_final: 0.8450 (tp30) REVERT: d 100 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8305 (mt-10) REVERT: d 140 LYS cc_start: 0.8583 (mtmm) cc_final: 0.7639 (pptt) REVERT: d 290 THR cc_start: 0.8806 (t) cc_final: 0.8589 (m) REVERT: e 39 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7788 (mtp-110) REVERT: e 74 LYS cc_start: 0.8181 (mttp) cc_final: 0.7855 (mmtt) REVERT: f 32 ASP cc_start: 0.8997 (t0) cc_final: 0.8731 (t0) REVERT: f 70 GLN cc_start: 0.8727 (pt0) cc_final: 0.8369 (pt0) REVERT: h 8 GLN cc_start: 0.9207 (tt0) cc_final: 0.8938 (mt0) REVERT: i 7 LEU cc_start: 0.8894 (mt) cc_final: 0.8420 (mp) REVERT: i 32 ASP cc_start: 0.8700 (t70) cc_final: 0.8360 (t0) REVERT: i 135 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8176 (mt0) REVERT: j 20 LYS cc_start: 0.8107 (tmmt) cc_final: 0.7852 (mttt) REVERT: j 29 LYS cc_start: 0.7726 (tttp) cc_final: 0.7207 (ttpp) REVERT: j 39 ASP cc_start: 0.7427 (m-30) cc_final: 0.7127 (t0) REVERT: j 82 ASP cc_start: 0.7354 (m-30) cc_final: 0.6760 (p0) REVERT: k 16 LYS cc_start: 0.8237 (mttt) cc_final: 0.7906 (mmtt) REVERT: k 94 TYR cc_start: 0.8709 (t80) cc_final: 0.8236 (t80) REVERT: k 134 PHE cc_start: 0.9022 (m-80) cc_final: 0.8689 (m-80) REVERT: k 135 LEU cc_start: 0.9083 (tp) cc_final: 0.8879 (tt) REVERT: k 173 ASP cc_start: 0.6985 (m-30) cc_final: 0.5886 (t0) REVERT: k 185 LYS cc_start: 0.7508 (mtmp) cc_final: 0.7131 (tppt) REVERT: l 4 ASP cc_start: 0.8845 (t0) cc_final: 0.8584 (t70) REVERT: l 87 LYS cc_start: 0.6813 (mmtt) cc_final: 0.6051 (mmmt) REVERT: m 14 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7615 (mmtm) REVERT: m 30 ILE cc_start: 0.8835 (pp) cc_final: 0.8502 (mt) REVERT: m 71 ASP cc_start: 0.7697 (m-30) cc_final: 0.7158 (m-30) REVERT: n 22 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7385 (mmmt) REVERT: p 65 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8621 (mp) REVERT: r 8 LYS cc_start: 0.8406 (mtpt) cc_final: 0.7804 (tppt) REVERT: r 98 GLU cc_start: 0.8436 (tt0) cc_final: 0.8123 (mt-10) REVERT: s 57 TYR cc_start: 0.7475 (m-80) cc_final: 0.7269 (m-80) REVERT: s 62 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8194 (tt) REVERT: u 58 GLN cc_start: 0.7348 (pm20) cc_final: 0.7131 (pm20) REVERT: v 8 MET cc_start: 0.7065 (ttp) cc_final: 0.6828 (tmm) REVERT: w 49 LYS cc_start: 0.8304 (ptpp) cc_final: 0.8029 (mtmm) REVERT: w 54 ASP cc_start: 0.8894 (t70) cc_final: 0.8390 (t0) REVERT: w 98 LYS cc_start: 0.7983 (tmtp) cc_final: 0.7734 (tmtt) REVERT: y 24 TYR cc_start: 0.8081 (t80) cc_final: 0.7794 (t80) REVERT: y 28 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7113 (mtm110) REVERT: y 49 LYS cc_start: 0.7140 (mtmt) cc_final: 0.6798 (mttp) outliers start: 205 outliers final: 154 residues processed: 1396 average time/residue: 0.6484 time to fit residues: 1533.4340 Evaluate side-chains 1384 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1219 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 442 VAL Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 82 LEU Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 365 THR Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 475 MET Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 525 LEU Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 49 ASN Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 148 SER Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain n residue 79 VAL Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 116 ASP Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain u residue 37 LEU Chi-restraints excluded: chain u residue 57 SER Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 115 MET Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 20.0000 chunk 692 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 451 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 769 optimal weight: 6.9990 chunk 638 optimal weight: 30.0000 chunk 356 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 403 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN 6 82 GLN H 235 ASN H 287 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 HIS L 296 ASN ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN d 36 ASN ** h 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 ASN t 12 GLN t 72 HIS u 6 HIS v 132 GLN y 13 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 68996 Z= 0.538 Angle : 1.559 50.602 93232 Z= 1.011 Chirality : 0.310 6.367 10101 Planarity : 0.004 0.056 11630 Dihedral : 11.197 171.267 10496 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.69 % Allowed : 12.67 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.25 (0.09), residues: 8036 helix: 0.95 (0.08), residues: 4228 sheet: -1.02 (0.25), residues: 406 loop : -0.59 (0.11), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 144 HIS 0.006 0.001 HIS Z 55 PHE 0.031 0.001 PHE N 292 TYR 0.028 0.001 TYR d 145 ARG 0.009 0.000 ARG i 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1266 time to evaluate : 6.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 82 MET cc_start: 0.9065 (mmm) cc_final: 0.8799 (mtp) REVERT: 1 249 ARG cc_start: 0.7912 (mpp-170) cc_final: 0.7517 (mtm-85) REVERT: 1 383 ASP cc_start: 0.9228 (t0) cc_final: 0.8867 (t0) REVERT: 1 431 GLN cc_start: 0.8067 (pt0) cc_final: 0.7736 (tt0) REVERT: 2 112 ASN cc_start: 0.8737 (t0) cc_final: 0.8401 (t0) REVERT: 2 114 ASP cc_start: 0.8740 (m-30) cc_final: 0.8533 (m-30) REVERT: 2 127 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8402 (mtpp) REVERT: 3 31 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8034 (mp0) REVERT: 3 418 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7889 (ttp80) REVERT: 3 475 GLN cc_start: 0.7148 (mm110) cc_final: 0.6596 (mp10) REVERT: 4 82 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8648 (mp) REVERT: 4 275 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7836 (p90) REVERT: 5 10 THR cc_start: 0.9009 (p) cc_final: 0.8781 (t) REVERT: 5 147 ASP cc_start: 0.7918 (t0) cc_final: 0.7141 (p0) REVERT: 5 178 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7911 (t0) REVERT: 6 70 ASP cc_start: 0.9099 (t70) cc_final: 0.8822 (t0) REVERT: 6 106 GLN cc_start: 0.8288 (mt0) cc_final: 0.8041 (mm110) REVERT: 9 78 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8756 (pp) REVERT: 9 118 TYR cc_start: 0.9160 (m-80) cc_final: 0.8883 (m-80) REVERT: A 23 TRP cc_start: 0.6659 (m100) cc_final: 0.6431 (m100) REVERT: A 108 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8056 (tm-30) REVERT: H 235 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8690 (m110) REVERT: H 270 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8165 (t80) REVERT: J 99 MET cc_start: 0.5973 (mmt) cc_final: 0.5559 (mtp) REVERT: J 118 LYS cc_start: 0.8029 (ttpt) cc_final: 0.7097 (mppt) REVERT: K 22 TYR cc_start: 0.8308 (m-10) cc_final: 0.7943 (m-10) REVERT: L 480 MET cc_start: 0.7403 (mmm) cc_final: 0.6587 (mmm) REVERT: L 488 MET cc_start: 0.7906 (mmm) cc_final: 0.7191 (ptt) REVERT: L 525 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7640 (mm) REVERT: L 540 MET cc_start: 0.7756 (mtm) cc_final: 0.6716 (mmt) REVERT: L 544 MET cc_start: 0.7006 (tmm) cc_final: 0.6401 (mmt) REVERT: L 547 LYS cc_start: 0.7962 (mttm) cc_final: 0.7095 (tmmt) REVERT: L 561 ILE cc_start: 0.7000 (pt) cc_final: 0.6787 (pt) REVERT: L 601 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7017 (tt) REVERT: M 36 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9031 (tt) REVERT: N 11 MET cc_start: 0.8524 (mmp) cc_final: 0.7919 (mtp) REVERT: N 151 LEU cc_start: 0.8821 (tp) cc_final: 0.8484 (tp) REVERT: V 7 GLN cc_start: 0.6111 (pt0) cc_final: 0.5621 (mt0) REVERT: W 102 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: X 68 GLU cc_start: 0.6363 (pt0) cc_final: 0.5674 (tp30) REVERT: Y 64 GLN cc_start: 0.8355 (tt0) cc_final: 0.8016 (mt0) REVERT: Y 79 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: Y 141 TYR cc_start: 0.9228 (m-80) cc_final: 0.8985 (m-80) REVERT: Z 5 ASP cc_start: 0.8531 (t0) cc_final: 0.8277 (t0) REVERT: a 72 SER cc_start: 0.9046 (p) cc_final: 0.8790 (m) REVERT: b 34 GLU cc_start: 0.8725 (tt0) cc_final: 0.8464 (tp30) REVERT: c 112 LYS cc_start: 0.8793 (pttt) cc_final: 0.8550 (pttp) REVERT: d 100 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: d 140 LYS cc_start: 0.8583 (mtmm) cc_final: 0.7664 (pptt) REVERT: d 290 THR cc_start: 0.8824 (t) cc_final: 0.8613 (m) REVERT: e 39 ARG cc_start: 0.8429 (mtt180) cc_final: 0.7775 (mtp-110) REVERT: e 74 LYS cc_start: 0.8158 (mttp) cc_final: 0.7833 (mmtt) REVERT: f 32 ASP cc_start: 0.8989 (t0) cc_final: 0.8727 (t0) REVERT: f 70 GLN cc_start: 0.8675 (pt0) cc_final: 0.8333 (pt0) REVERT: h 8 GLN cc_start: 0.9171 (tt0) cc_final: 0.8898 (mt0) REVERT: i 7 LEU cc_start: 0.8888 (mt) cc_final: 0.8395 (mp) REVERT: i 32 ASP cc_start: 0.8644 (t70) cc_final: 0.8299 (t0) REVERT: i 135 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8154 (mt0) REVERT: j 20 LYS cc_start: 0.8095 (tmmt) cc_final: 0.7844 (mttt) REVERT: j 29 LYS cc_start: 0.7787 (tttp) cc_final: 0.7153 (ttpp) REVERT: j 39 ASP cc_start: 0.7416 (m-30) cc_final: 0.7114 (t0) REVERT: j 78 ASP cc_start: 0.7990 (m-30) cc_final: 0.7694 (m-30) REVERT: j 82 ASP cc_start: 0.7377 (m-30) cc_final: 0.6783 (p0) REVERT: k 16 LYS cc_start: 0.8203 (mttt) cc_final: 0.7890 (mmtt) REVERT: k 58 TYR cc_start: 0.8270 (t80) cc_final: 0.8066 (t80) REVERT: k 94 TYR cc_start: 0.8697 (t80) cc_final: 0.8220 (t80) REVERT: k 135 LEU cc_start: 0.9085 (tp) cc_final: 0.8696 (tt) REVERT: k 162 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7847 (mt-10) REVERT: k 185 LYS cc_start: 0.7554 (mtmp) cc_final: 0.7156 (tppt) REVERT: l 4 ASP cc_start: 0.8813 (t0) cc_final: 0.8568 (t0) REVERT: l 37 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8547 (tttm) REVERT: l 87 LYS cc_start: 0.6754 (mmtt) cc_final: 0.5957 (mmmt) REVERT: m 14 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7857 (mptt) REVERT: m 30 ILE cc_start: 0.8804 (pp) cc_final: 0.8502 (mt) REVERT: m 71 ASP cc_start: 0.7647 (m-30) cc_final: 0.7131 (m-30) REVERT: n 22 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7400 (mmmt) REVERT: p 65 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8599 (mp) REVERT: r 8 LYS cc_start: 0.8376 (mtpt) cc_final: 0.7788 (tppt) REVERT: r 98 GLU cc_start: 0.8452 (tt0) cc_final: 0.8160 (mt-10) REVERT: s 38 MET cc_start: 0.6661 (tpt) cc_final: 0.6354 (mmm) REVERT: s 62 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8165 (tt) REVERT: t 10 THR cc_start: 0.7372 (p) cc_final: 0.6941 (p) REVERT: u 58 GLN cc_start: 0.7392 (pm20) cc_final: 0.7142 (pm20) REVERT: v 8 MET cc_start: 0.7060 (ttp) cc_final: 0.6817 (tmm) REVERT: v 89 VAL cc_start: 0.7930 (p) cc_final: 0.7692 (m) REVERT: w 54 ASP cc_start: 0.8836 (t70) cc_final: 0.8326 (t0) REVERT: w 56 TRP cc_start: 0.8123 (t-100) cc_final: 0.7886 (t-100) REVERT: w 98 LYS cc_start: 0.7979 (tmtp) cc_final: 0.7759 (tmtt) REVERT: y 24 TYR cc_start: 0.8013 (t80) cc_final: 0.7766 (t80) REVERT: y 28 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.7081 (mtm110) outliers start: 192 outliers final: 135 residues processed: 1386 average time/residue: 0.6528 time to fit residues: 1534.8625 Evaluate side-chains 1360 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1210 time to evaluate : 6.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 24 THR Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 82 LEU Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 73 LYS Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 112 ASP Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 235 ASN Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 525 LEU Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain l residue 37 LYS Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 48 GLU Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 134 SER Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 115 MET Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 438 optimal weight: 40.0000 chunk 561 optimal weight: 6.9990 chunk 435 optimal weight: 30.0000 chunk 647 optimal weight: 0.0470 chunk 429 optimal weight: 9.9990 chunk 766 optimal weight: 9.9990 chunk 479 optimal weight: 20.0000 chunk 467 optimal weight: 0.6980 chunk 353 optimal weight: 10.0000 overall best weight: 5.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN 6 82 GLN H 235 ASN H 287 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 ASN Y 72 GLN g 94 ASN ** h 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 ASN p 51 ASN t 72 HIS u 6 HIS v 155 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.240 68996 Z= 0.570 Angle : 1.573 50.672 93232 Z= 1.016 Chirality : 0.310 6.376 10101 Planarity : 0.004 0.059 11630 Dihedral : 11.159 171.795 10496 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.93 % Allowed : 13.02 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.28 (0.09), residues: 8036 helix: 0.96 (0.08), residues: 4225 sheet: -0.99 (0.25), residues: 405 loop : -0.55 (0.11), residues: 3406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 144 HIS 0.008 0.001 HIS u 50 PHE 0.031 0.002 PHE N 292 TYR 0.034 0.001 TYR d 145 ARG 0.008 0.000 ARG i 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1240 time to evaluate : 6.799 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: 1 82 MET cc_start: 0.9063 (mmm) cc_final: 0.8827 (mtp) REVERT: 1 249 ARG cc_start: 0.7922 (mpp-170) cc_final: 0.7534 (mtm-85) REVERT: 1 425 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8147 (tt0) REVERT: 1 431 GLN cc_start: 0.8087 (pt0) cc_final: 0.7760 (tt0) REVERT: 2 112 ASN cc_start: 0.8720 (t0) cc_final: 0.8453 (t0) REVERT: 2 114 ASP cc_start: 0.8762 (m-30) cc_final: 0.8560 (m-30) REVERT: 2 127 LYS cc_start: 0.8770 (ptpt) cc_final: 0.8448 (mtpp) REVERT: 3 31 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8028 (mp0) REVERT: 3 71 MET cc_start: 0.9192 (tpp) cc_final: 0.8974 (tpt) REVERT: 3 418 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7868 (ttp80) REVERT: 3 475 GLN cc_start: 0.7175 (mm110) cc_final: 0.6589 (mp10) REVERT: 4 82 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8695 (mp) REVERT: 4 152 MET cc_start: 0.8694 (ttt) cc_final: 0.8436 (ttt) REVERT: 4 275 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7933 (p90) REVERT: 5 147 ASP cc_start: 0.7982 (t0) cc_final: 0.7195 (p0) REVERT: 5 178 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7918 (t0) REVERT: 6 70 ASP cc_start: 0.9126 (t70) cc_final: 0.8836 (t0) REVERT: 6 106 GLN cc_start: 0.8378 (mt0) cc_final: 0.8107 (mm110) REVERT: 9 78 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 23 TRP cc_start: 0.6739 (m100) cc_final: 0.6535 (m100) REVERT: A 108 GLN cc_start: 0.8819 (mm-40) cc_final: 0.7940 (tm-30) REVERT: H 270 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8072 (t80) REVERT: J 99 MET cc_start: 0.5953 (mmt) cc_final: 0.5544 (mtp) REVERT: J 118 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7118 (mppt) REVERT: L 102 GLU cc_start: 0.8496 (tt0) cc_final: 0.8291 (tt0) REVERT: L 343 SER cc_start: 0.9087 (t) cc_final: 0.8695 (t) REVERT: L 359 MET cc_start: 0.8284 (mtt) cc_final: 0.8026 (mtm) REVERT: L 425 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7292 (ttt180) REVERT: L 488 MET cc_start: 0.7950 (mmm) cc_final: 0.7203 (ptt) REVERT: L 525 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7635 (mm) REVERT: L 540 MET cc_start: 0.7753 (mtm) cc_final: 0.6768 (mmt) REVERT: L 544 MET cc_start: 0.6942 (tmm) cc_final: 0.6388 (mmt) REVERT: L 547 LYS cc_start: 0.8060 (mttm) cc_final: 0.7136 (tmmt) REVERT: L 561 ILE cc_start: 0.7009 (pt) cc_final: 0.6805 (pt) REVERT: L 601 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6990 (tt) REVERT: M 36 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9050 (tt) REVERT: M 396 MET cc_start: 0.8388 (mmt) cc_final: 0.8092 (mmm) REVERT: N 11 MET cc_start: 0.8510 (mmp) cc_final: 0.7876 (mtp) REVERT: N 151 LEU cc_start: 0.8859 (tp) cc_final: 0.8588 (tp) REVERT: V 7 GLN cc_start: 0.6068 (pt0) cc_final: 0.5606 (mt0) REVERT: W 102 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: X 68 GLU cc_start: 0.6391 (pt0) cc_final: 0.5735 (tp30) REVERT: Y 64 GLN cc_start: 0.8386 (tt0) cc_final: 0.8146 (mt0) REVERT: Y 141 TYR cc_start: 0.9228 (m-80) cc_final: 0.8993 (m-80) REVERT: Z 5 ASP cc_start: 0.8553 (t0) cc_final: 0.8301 (t0) REVERT: Z 66 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7292 (mm-30) REVERT: a 72 SER cc_start: 0.9095 (p) cc_final: 0.8808 (m) REVERT: d 100 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8327 (mt-10) REVERT: d 140 LYS cc_start: 0.8661 (mtmm) cc_final: 0.7695 (pptt) REVERT: d 290 THR cc_start: 0.8815 (t) cc_final: 0.8609 (m) REVERT: e 39 ARG cc_start: 0.8526 (mtt180) cc_final: 0.7790 (mtp-110) REVERT: e 74 LYS cc_start: 0.8183 (mttp) cc_final: 0.7865 (mmtt) REVERT: f 32 ASP cc_start: 0.8980 (t0) cc_final: 0.8724 (t0) REVERT: f 57 ILE cc_start: 0.8330 (mm) cc_final: 0.8090 (mm) REVERT: f 70 GLN cc_start: 0.8720 (pt0) cc_final: 0.8375 (pt0) REVERT: h 8 GLN cc_start: 0.9184 (tt0) cc_final: 0.8904 (mt0) REVERT: h 92 LYS cc_start: 0.8417 (mptt) cc_final: 0.8056 (mmmm) REVERT: i 7 LEU cc_start: 0.8874 (mt) cc_final: 0.8389 (mp) REVERT: i 32 ASP cc_start: 0.8705 (t70) cc_final: 0.8350 (t0) REVERT: i 135 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8155 (mt0) REVERT: j 20 LYS cc_start: 0.8106 (tmmt) cc_final: 0.7861 (mttt) REVERT: j 29 LYS cc_start: 0.7804 (tttp) cc_final: 0.7172 (ttpp) REVERT: j 39 ASP cc_start: 0.7462 (m-30) cc_final: 0.7174 (t0) REVERT: j 78 ASP cc_start: 0.8021 (m-30) cc_final: 0.7647 (m-30) REVERT: j 82 ASP cc_start: 0.7396 (m-30) cc_final: 0.6776 (p0) REVERT: k 16 LYS cc_start: 0.8192 (mttt) cc_final: 0.7880 (mmtt) REVERT: k 58 TYR cc_start: 0.8335 (t80) cc_final: 0.8132 (t80) REVERT: k 135 LEU cc_start: 0.9122 (tp) cc_final: 0.8908 (tt) REVERT: k 162 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7850 (mt-10) REVERT: k 185 LYS cc_start: 0.7561 (mtmp) cc_final: 0.7145 (tppt) REVERT: l 4 ASP cc_start: 0.8866 (t0) cc_final: 0.8622 (t0) REVERT: l 37 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8578 (tttm) REVERT: l 87 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6019 (mmmt) REVERT: m 14 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7863 (mptt) REVERT: m 30 ILE cc_start: 0.8818 (pp) cc_final: 0.8504 (mt) REVERT: m 71 ASP cc_start: 0.7646 (m-30) cc_final: 0.7105 (m-30) REVERT: n 22 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7392 (mmmt) REVERT: p 65 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8581 (mp) REVERT: r 8 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7753 (tppt) REVERT: r 12 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7994 (mm-40) REVERT: r 98 GLU cc_start: 0.8503 (tt0) cc_final: 0.8236 (mt-10) REVERT: s 62 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8218 (tt) REVERT: t 10 THR cc_start: 0.7399 (p) cc_final: 0.6967 (p) REVERT: u 35 TRP cc_start: 0.8625 (t-100) cc_final: 0.8311 (t-100) REVERT: u 58 GLN cc_start: 0.7353 (pm20) cc_final: 0.7094 (pm20) REVERT: v 8 MET cc_start: 0.7059 (ttp) cc_final: 0.6808 (tmm) REVERT: v 87 ASN cc_start: 0.8779 (m110) cc_final: 0.8514 (m110) REVERT: v 89 VAL cc_start: 0.7932 (p) cc_final: 0.7708 (m) REVERT: w 54 ASP cc_start: 0.8864 (t70) cc_final: 0.8348 (t0) REVERT: w 98 LYS cc_start: 0.7995 (tmtp) cc_final: 0.7776 (tmtt) REVERT: y 24 TYR cc_start: 0.8056 (t80) cc_final: 0.7782 (t80) REVERT: y 28 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.7007 (mtm110) outliers start: 209 outliers final: 163 residues processed: 1373 average time/residue: 0.6497 time to fit residues: 1511.4845 Evaluate side-chains 1385 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1207 time to evaluate : 6.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 1 residue 355 LYS Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 82 LEU Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 16 ASP Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 73 LYS Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 112 ASP Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 475 MET Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 525 LEU Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 49 ASN Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 90 GLN Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 206 TYR Chi-restraints excluded: chain l residue 37 LYS Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 2 MET Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain p residue 127 SER Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 12 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 116 ASP Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 115 MET Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 8.9990 chunk 305 optimal weight: 0.9980 chunk 457 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 487 optimal weight: 20.0000 chunk 522 optimal weight: 4.9990 chunk 378 optimal weight: 5.9990 chunk 71 optimal weight: 0.0670 chunk 602 optimal weight: 7.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN H 287 HIS L 23 ASN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN c 44 ASN ** h 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 ASN t 72 HIS u 6 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68996 Z= 0.544 Angle : 1.563 50.625 93232 Z= 1.012 Chirality : 0.310 6.363 10101 Planarity : 0.004 0.057 11630 Dihedral : 10.979 171.505 10496 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.76 % Allowed : 13.43 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.41 (0.10), residues: 8036 helix: 1.06 (0.08), residues: 4226 sheet: -0.91 (0.25), residues: 410 loop : -0.49 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 144 HIS 0.005 0.001 HIS 3 101 PHE 0.031 0.001 PHE N 292 TYR 0.034 0.001 TYR d 145 ARG 0.009 0.000 ARG i 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1242 time to evaluate : 6.072 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: 1 82 MET cc_start: 0.9075 (mmm) cc_final: 0.8871 (mtp) REVERT: 1 249 ARG cc_start: 0.7929 (mpp-170) cc_final: 0.7546 (mtm-85) REVERT: 1 383 ASP cc_start: 0.9228 (t0) cc_final: 0.8916 (t0) REVERT: 1 425 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8169 (tt0) REVERT: 1 431 GLN cc_start: 0.8079 (pt0) cc_final: 0.7749 (tt0) REVERT: 2 112 ASN cc_start: 0.8724 (t0) cc_final: 0.8464 (t0) REVERT: 2 114 ASP cc_start: 0.8726 (m-30) cc_final: 0.8524 (m-30) REVERT: 2 127 LYS cc_start: 0.8768 (ptpt) cc_final: 0.8440 (mtpp) REVERT: 3 31 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8012 (mp0) REVERT: 3 71 MET cc_start: 0.9185 (tpp) cc_final: 0.8964 (tpt) REVERT: 3 418 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7871 (ttp80) REVERT: 3 475 GLN cc_start: 0.7180 (mm110) cc_final: 0.6614 (mp10) REVERT: 4 82 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8650 (mp) REVERT: 4 152 MET cc_start: 0.8673 (ttt) cc_final: 0.8425 (ttt) REVERT: 4 275 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7893 (p90) REVERT: 5 10 THR cc_start: 0.8977 (p) cc_final: 0.8720 (t) REVERT: 5 147 ASP cc_start: 0.7987 (t0) cc_final: 0.7215 (p0) REVERT: 5 178 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7914 (t0) REVERT: 6 70 ASP cc_start: 0.9111 (t70) cc_final: 0.8846 (t0) REVERT: 6 102 LYS cc_start: 0.9093 (tttt) cc_final: 0.8852 (tttp) REVERT: 6 106 GLN cc_start: 0.8367 (mt0) cc_final: 0.8099 (mm110) REVERT: 9 78 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8746 (pp) REVERT: A 108 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8119 (tm-30) REVERT: H 270 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8136 (t80) REVERT: J 99 MET cc_start: 0.5949 (mmt) cc_final: 0.5538 (mtp) REVERT: J 118 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7103 (mppt) REVERT: L 343 SER cc_start: 0.9045 (t) cc_final: 0.8651 (t) REVERT: L 425 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7608 (ttt180) REVERT: L 488 MET cc_start: 0.7939 (mmm) cc_final: 0.7199 (ptt) REVERT: L 525 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7692 (mm) REVERT: L 540 MET cc_start: 0.7806 (mtm) cc_final: 0.6751 (mmt) REVERT: L 544 MET cc_start: 0.6920 (tmm) cc_final: 0.6354 (mmt) REVERT: L 547 LYS cc_start: 0.8019 (mttm) cc_final: 0.7110 (tmmt) REVERT: L 601 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7045 (tt) REVERT: M 36 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9032 (tt) REVERT: M 396 MET cc_start: 0.8360 (mmt) cc_final: 0.8073 (mmm) REVERT: N 11 MET cc_start: 0.8525 (mmp) cc_final: 0.7887 (mtp) REVERT: N 151 LEU cc_start: 0.8821 (tp) cc_final: 0.8552 (tp) REVERT: V 7 GLN cc_start: 0.6099 (pt0) cc_final: 0.5605 (mt0) REVERT: W 102 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: X 68 GLU cc_start: 0.6390 (pt0) cc_final: 0.5768 (tp30) REVERT: Y 64 GLN cc_start: 0.8393 (tt0) cc_final: 0.8065 (mt0) REVERT: Y 79 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: Y 112 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: Y 141 TYR cc_start: 0.9172 (m-80) cc_final: 0.8904 (m-80) REVERT: Z 66 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: a 72 SER cc_start: 0.9050 (p) cc_final: 0.8806 (m) REVERT: b 7 THR cc_start: 0.8819 (m) cc_final: 0.8607 (m) REVERT: c 112 LYS cc_start: 0.8814 (pttt) cc_final: 0.8583 (pttp) REVERT: d 100 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8224 (mt-10) REVERT: d 140 LYS cc_start: 0.8598 (mtmm) cc_final: 0.7970 (pptt) REVERT: d 290 THR cc_start: 0.8819 (t) cc_final: 0.8609 (m) REVERT: e 39 ARG cc_start: 0.8510 (mtt180) cc_final: 0.7793 (mtp-110) REVERT: e 74 LYS cc_start: 0.8175 (mttp) cc_final: 0.7862 (mmtt) REVERT: f 32 ASP cc_start: 0.8978 (t0) cc_final: 0.8729 (t0) REVERT: f 57 ILE cc_start: 0.8319 (mm) cc_final: 0.8061 (mm) REVERT: f 70 GLN cc_start: 0.8693 (pt0) cc_final: 0.8377 (pt0) REVERT: h 8 GLN cc_start: 0.9152 (tt0) cc_final: 0.8884 (mt0) REVERT: h 92 LYS cc_start: 0.8448 (mptt) cc_final: 0.8071 (mmtm) REVERT: i 7 LEU cc_start: 0.8856 (mt) cc_final: 0.8360 (mp) REVERT: i 32 ASP cc_start: 0.8687 (t70) cc_final: 0.8316 (t0) REVERT: i 135 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8152 (mt0) REVERT: j 20 LYS cc_start: 0.8103 (tmmt) cc_final: 0.7892 (mttt) REVERT: j 29 LYS cc_start: 0.7782 (tttp) cc_final: 0.7170 (ttpp) REVERT: j 39 ASP cc_start: 0.7460 (m-30) cc_final: 0.7179 (t0) REVERT: j 78 ASP cc_start: 0.8005 (m-30) cc_final: 0.7683 (m-30) REVERT: j 82 ASP cc_start: 0.7366 (m-30) cc_final: 0.6761 (p0) REVERT: k 58 TYR cc_start: 0.8291 (t80) cc_final: 0.7957 (t80) REVERT: k 94 TYR cc_start: 0.8747 (t80) cc_final: 0.8284 (t80) REVERT: k 135 LEU cc_start: 0.9120 (tp) cc_final: 0.8919 (tt) REVERT: k 162 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7888 (mt-10) REVERT: k 185 LYS cc_start: 0.7577 (mtmp) cc_final: 0.7126 (tppt) REVERT: l 4 ASP cc_start: 0.8850 (t0) cc_final: 0.8623 (t0) REVERT: l 37 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8538 (tttm) REVERT: l 87 LYS cc_start: 0.6779 (mmtt) cc_final: 0.5997 (mmmt) REVERT: m 14 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7829 (mptt) REVERT: m 30 ILE cc_start: 0.8804 (pp) cc_final: 0.8508 (mt) REVERT: m 71 ASP cc_start: 0.7662 (m-30) cc_final: 0.7138 (m-30) REVERT: n 22 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7401 (mmmt) REVERT: p 65 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8582 (mp) REVERT: r 8 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7754 (tppt) REVERT: r 98 GLU cc_start: 0.8514 (tt0) cc_final: 0.8234 (mt-10) REVERT: s 62 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8178 (tt) REVERT: t 10 THR cc_start: 0.7422 (p) cc_final: 0.7005 (p) REVERT: u 14 PHE cc_start: 0.7842 (t80) cc_final: 0.7358 (t80) REVERT: u 35 TRP cc_start: 0.8603 (t-100) cc_final: 0.8322 (t-100) REVERT: u 58 GLN cc_start: 0.7298 (pm20) cc_final: 0.7069 (pm20) REVERT: v 8 MET cc_start: 0.7012 (ttp) cc_final: 0.6786 (tmm) REVERT: v 87 ASN cc_start: 0.8771 (m110) cc_final: 0.8509 (m110) REVERT: w 28 GLU cc_start: 0.7975 (tp30) cc_final: 0.7116 (pt0) REVERT: w 54 ASP cc_start: 0.8843 (t70) cc_final: 0.8328 (t0) REVERT: w 56 TRP cc_start: 0.8150 (t-100) cc_final: 0.7912 (t-100) REVERT: w 98 LYS cc_start: 0.7976 (tmtp) cc_final: 0.7757 (tttp) REVERT: y 24 TYR cc_start: 0.8011 (t80) cc_final: 0.7741 (t80) REVERT: y 28 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.6790 (mtm110) outliers start: 197 outliers final: 152 residues processed: 1364 average time/residue: 0.6735 time to fit residues: 1564.3692 Evaluate side-chains 1379 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1211 time to evaluate : 5.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 201 ASP Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 82 LEU Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 16 ASP Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 73 LYS Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 112 ASP Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 525 LEU Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain l residue 37 LYS Chi-restraints excluded: chain l residue 92 THR Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 115 MET Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 48 MET Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.0170 chunk 734 optimal weight: 20.0000 chunk 669 optimal weight: 30.0000 chunk 714 optimal weight: 5.9990 chunk 733 optimal weight: 8.9990 chunk 429 optimal weight: 5.9990 chunk 311 optimal weight: 0.9990 chunk 560 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 645 optimal weight: 8.9990 chunk 675 optimal weight: 4.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Y 142 HIS a 40 ASN g 94 ASN ** h 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 ASN t 72 HIS u 6 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68996 Z= 0.543 Angle : 1.564 50.621 93232 Z= 1.012 Chirality : 0.310 6.360 10101 Planarity : 0.004 0.064 11630 Dihedral : 10.830 171.032 10496 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.82 % Allowed : 13.53 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.49 (0.10), residues: 8036 helix: 1.14 (0.08), residues: 4212 sheet: -0.88 (0.25), residues: 405 loop : -0.46 (0.11), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP t 71 HIS 0.005 0.001 HIS 3 101 PHE 0.031 0.001 PHE N 292 TYR 0.035 0.001 TYR d 145 ARG 0.015 0.000 ARG l 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1249 time to evaluate : 5.995 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: 1 82 MET cc_start: 0.9087 (mmm) cc_final: 0.8874 (mtp) REVERT: 1 249 ARG cc_start: 0.7918 (mpp-170) cc_final: 0.7539 (mtm-85) REVERT: 1 383 ASP cc_start: 0.9224 (t0) cc_final: 0.8911 (t0) REVERT: 1 431 GLN cc_start: 0.8075 (pt0) cc_final: 0.7745 (tt0) REVERT: 2 112 ASN cc_start: 0.8705 (t0) cc_final: 0.8449 (t0) REVERT: 2 114 ASP cc_start: 0.8726 (m-30) cc_final: 0.8521 (m-30) REVERT: 2 127 LYS cc_start: 0.8766 (ptpt) cc_final: 0.8441 (mtpp) REVERT: 3 31 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8010 (mp0) REVERT: 3 71 MET cc_start: 0.9179 (tpp) cc_final: 0.8958 (tpt) REVERT: 3 253 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8661 (mtm180) REVERT: 3 418 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7895 (ttp80) REVERT: 3 475 GLN cc_start: 0.7168 (mm110) cc_final: 0.6639 (mp10) REVERT: 4 50 ASN cc_start: 0.8728 (t0) cc_final: 0.8507 (t0) REVERT: 4 152 MET cc_start: 0.8686 (ttt) cc_final: 0.8449 (ttt) REVERT: 4 275 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7852 (p90) REVERT: 5 10 THR cc_start: 0.8986 (p) cc_final: 0.8731 (t) REVERT: 5 147 ASP cc_start: 0.7988 (t0) cc_final: 0.7233 (p0) REVERT: 5 178 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7938 (t0) REVERT: 6 70 ASP cc_start: 0.9097 (t70) cc_final: 0.8843 (t0) REVERT: 6 102 LYS cc_start: 0.9079 (tttt) cc_final: 0.8839 (tttp) REVERT: 6 106 GLN cc_start: 0.8409 (mt0) cc_final: 0.8105 (mm110) REVERT: 9 78 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8749 (pp) REVERT: A 23 TRP cc_start: 0.6758 (m100) cc_final: 0.6219 (m-10) REVERT: A 108 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8162 (tm-30) REVERT: H 194 ASN cc_start: 0.8386 (m-40) cc_final: 0.7544 (t0) REVERT: H 270 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8144 (t80) REVERT: J 99 MET cc_start: 0.5949 (mmt) cc_final: 0.5539 (mtp) REVERT: J 118 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7109 (mppt) REVERT: K 21 MET cc_start: 0.8420 (mtp) cc_final: 0.8146 (mtm) REVERT: L 343 SER cc_start: 0.9021 (t) cc_final: 0.8640 (t) REVERT: L 359 MET cc_start: 0.8222 (mtt) cc_final: 0.7901 (mtm) REVERT: L 425 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7694 (ttt180) REVERT: L 488 MET cc_start: 0.7934 (mmm) cc_final: 0.7199 (ptt) REVERT: L 525 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7747 (mm) REVERT: L 540 MET cc_start: 0.7732 (mtm) cc_final: 0.6798 (mmt) REVERT: L 544 MET cc_start: 0.6909 (tmm) cc_final: 0.6340 (mmt) REVERT: L 547 LYS cc_start: 0.8066 (mttm) cc_final: 0.7130 (tmmt) REVERT: L 601 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7043 (tt) REVERT: M 36 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9028 (tt) REVERT: M 396 MET cc_start: 0.8338 (mmt) cc_final: 0.8070 (mmm) REVERT: N 11 MET cc_start: 0.8500 (mmp) cc_final: 0.7865 (mtp) REVERT: N 151 LEU cc_start: 0.8824 (tp) cc_final: 0.8544 (tp) REVERT: N 294 MET cc_start: 0.8421 (tpp) cc_final: 0.8207 (tpt) REVERT: V 7 GLN cc_start: 0.6072 (pt0) cc_final: 0.5568 (mt0) REVERT: W 102 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: X 68 GLU cc_start: 0.6314 (pt0) cc_final: 0.5700 (tp30) REVERT: Y 64 GLN cc_start: 0.8407 (tt0) cc_final: 0.8080 (mt0) REVERT: Y 79 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: Y 112 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: Y 141 TYR cc_start: 0.9176 (m-80) cc_final: 0.8871 (m-80) REVERT: Z 66 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: a 72 SER cc_start: 0.9047 (p) cc_final: 0.8815 (m) REVERT: c 30 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8789 (mt) REVERT: c 112 LYS cc_start: 0.8811 (pttt) cc_final: 0.8573 (pttp) REVERT: d 100 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: d 140 LYS cc_start: 0.8606 (mtmm) cc_final: 0.7984 (pptt) REVERT: d 290 THR cc_start: 0.8815 (t) cc_final: 0.8610 (m) REVERT: e 39 ARG cc_start: 0.8516 (mtt180) cc_final: 0.7807 (mtp-110) REVERT: e 74 LYS cc_start: 0.8149 (mttp) cc_final: 0.7857 (mmtt) REVERT: f 32 ASP cc_start: 0.8974 (t0) cc_final: 0.8719 (t0) REVERT: f 57 ILE cc_start: 0.8324 (mm) cc_final: 0.8062 (mm) REVERT: f 70 GLN cc_start: 0.8694 (pt0) cc_final: 0.8434 (pt0) REVERT: h 8 GLN cc_start: 0.9154 (tt0) cc_final: 0.8906 (mt0) REVERT: h 92 LYS cc_start: 0.8463 (mptt) cc_final: 0.8081 (mmtm) REVERT: i 7 LEU cc_start: 0.8832 (mt) cc_final: 0.8329 (mp) REVERT: i 32 ASP cc_start: 0.8686 (t70) cc_final: 0.8305 (t0) REVERT: i 135 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8148 (mt0) REVERT: j 20 LYS cc_start: 0.8098 (tmmt) cc_final: 0.7886 (mttt) REVERT: j 29 LYS cc_start: 0.7762 (tttp) cc_final: 0.7155 (ttpp) REVERT: j 39 ASP cc_start: 0.7424 (m-30) cc_final: 0.7163 (t0) REVERT: j 78 ASP cc_start: 0.8038 (m-30) cc_final: 0.7704 (m-30) REVERT: j 82 ASP cc_start: 0.7414 (m-30) cc_final: 0.6798 (p0) REVERT: k 58 TYR cc_start: 0.8292 (t80) cc_final: 0.7968 (t80) REVERT: k 94 TYR cc_start: 0.8730 (t80) cc_final: 0.8328 (t80) REVERT: k 162 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7923 (mt-10) REVERT: k 185 LYS cc_start: 0.7561 (mtmp) cc_final: 0.7148 (tppt) REVERT: l 4 ASP cc_start: 0.8852 (t0) cc_final: 0.8614 (t0) REVERT: l 37 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8529 (tttm) REVERT: l 87 LYS cc_start: 0.6726 (mmtt) cc_final: 0.5967 (mmmt) REVERT: m 14 LYS cc_start: 0.8321 (mtmt) cc_final: 0.7609 (mmtt) REVERT: m 30 ILE cc_start: 0.8801 (pp) cc_final: 0.8517 (mt) REVERT: m 71 ASP cc_start: 0.7660 (m-30) cc_final: 0.7129 (m-30) REVERT: n 22 LYS cc_start: 0.7834 (mtmm) cc_final: 0.7397 (mmmt) REVERT: p 65 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8576 (mp) REVERT: r 8 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7773 (tppt) REVERT: r 12 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: r 98 GLU cc_start: 0.8513 (tt0) cc_final: 0.8232 (mt-10) REVERT: s 62 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8170 (tt) REVERT: t 10 THR cc_start: 0.7423 (p) cc_final: 0.6985 (p) REVERT: u 14 PHE cc_start: 0.7974 (t80) cc_final: 0.7487 (t80) REVERT: u 35 TRP cc_start: 0.8601 (t-100) cc_final: 0.8335 (t-100) REVERT: u 58 GLN cc_start: 0.7292 (pm20) cc_final: 0.7067 (pm20) REVERT: v 8 MET cc_start: 0.6958 (ttp) cc_final: 0.6742 (tmm) REVERT: v 87 ASN cc_start: 0.8764 (m110) cc_final: 0.8501 (m110) REVERT: w 28 GLU cc_start: 0.7873 (tp30) cc_final: 0.7114 (pt0) REVERT: w 54 ASP cc_start: 0.8852 (t70) cc_final: 0.8328 (t0) REVERT: w 56 TRP cc_start: 0.8124 (t-100) cc_final: 0.7889 (t-100) REVERT: y 24 TYR cc_start: 0.7975 (t80) cc_final: 0.7712 (t80) REVERT: y 28 ARG cc_start: 0.7577 (mmm-85) cc_final: 0.6897 (mtm110) outliers start: 201 outliers final: 164 residues processed: 1369 average time/residue: 0.6492 time to fit residues: 1507.8585 Evaluate side-chains 1391 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1209 time to evaluate : 7.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 201 ASP Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 253 ARG Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 16 ASP Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 73 LYS Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 112 ASP Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 263 SER Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain K residue 70 GLU Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 525 LEU Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 138 ASN Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 243 MET Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 90 GLN Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain l residue 37 LYS Chi-restraints excluded: chain l residue 92 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 81 VAL Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 12 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain u residue 48 LEU Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 115 MET Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 48 MET Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 30.0000 chunk 468 optimal weight: 7.9990 chunk 755 optimal weight: 9.9990 chunk 460 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 524 optimal weight: 6.9990 chunk 792 optimal weight: 8.9990 chunk 728 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 487 optimal weight: 20.0000 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 287 HIS ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN c 44 ASN g 47 HIS g 94 ASN ** h 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 271 ASN t 72 HIS t 140 GLN u 6 HIS v 66 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 68996 Z= 0.595 Angle : 1.589 50.724 93232 Z= 1.022 Chirality : 0.311 6.385 10101 Planarity : 0.004 0.058 11630 Dihedral : 11.028 172.376 10496 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.88 % Allowed : 13.71 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.09), residues: 8036 helix: 0.98 (0.08), residues: 4224 sheet: -0.92 (0.25), residues: 403 loop : -0.51 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP t 71 HIS 0.007 0.001 HIS g 47 PHE 0.030 0.002 PHE N 292 TYR 0.043 0.002 TYR d 145 ARG 0.010 0.001 ARG c 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1214 time to evaluate : 6.132 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: 1 82 MET cc_start: 0.9098 (mmm) cc_final: 0.8854 (mtp) REVERT: 1 249 ARG cc_start: 0.7926 (mpp-170) cc_final: 0.7476 (mtm-85) REVERT: 1 425 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8082 (tt0) REVERT: 1 431 GLN cc_start: 0.8077 (pt0) cc_final: 0.7754 (tt0) REVERT: 2 112 ASN cc_start: 0.8718 (t0) cc_final: 0.8445 (t0) REVERT: 2 114 ASP cc_start: 0.8776 (m-30) cc_final: 0.8572 (m-30) REVERT: 2 127 LYS cc_start: 0.8808 (ptpt) cc_final: 0.8425 (mtpp) REVERT: 3 31 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8023 (mp0) REVERT: 3 71 MET cc_start: 0.9200 (tpp) cc_final: 0.8977 (tpt) REVERT: 3 475 GLN cc_start: 0.7132 (mm110) cc_final: 0.6606 (mp10) REVERT: 4 50 ASN cc_start: 0.8854 (t0) cc_final: 0.8549 (t0) REVERT: 4 152 MET cc_start: 0.8725 (ttt) cc_final: 0.8456 (ttt) REVERT: 4 275 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.8009 (p90) REVERT: 5 10 THR cc_start: 0.8992 (p) cc_final: 0.8735 (t) REVERT: 5 147 ASP cc_start: 0.8051 (t0) cc_final: 0.7288 (p0) REVERT: 5 178 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8091 (t0) REVERT: 6 70 ASP cc_start: 0.9139 (t70) cc_final: 0.8837 (t0) REVERT: 6 102 LYS cc_start: 0.9097 (tttt) cc_final: 0.8853 (tttp) REVERT: 6 106 GLN cc_start: 0.8396 (mt0) cc_final: 0.8089 (mm110) REVERT: 9 78 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8797 (pp) REVERT: A 23 TRP cc_start: 0.6788 (m100) cc_final: 0.6288 (m-10) REVERT: H 97 ASN cc_start: 0.8204 (t0) cc_final: 0.7890 (t0) REVERT: H 194 ASN cc_start: 0.8486 (m-40) cc_final: 0.7652 (t0) REVERT: J 99 MET cc_start: 0.5991 (mmt) cc_final: 0.5593 (mtp) REVERT: J 118 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7110 (mppt) REVERT: L 343 SER cc_start: 0.9073 (t) cc_final: 0.8698 (t) REVERT: L 425 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7614 (ttt180) REVERT: L 488 MET cc_start: 0.7932 (mmm) cc_final: 0.7211 (ptt) REVERT: L 525 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7740 (mm) REVERT: L 540 MET cc_start: 0.7862 (mtm) cc_final: 0.6795 (mmt) REVERT: L 544 MET cc_start: 0.6847 (tmm) cc_final: 0.6285 (mmt) REVERT: L 547 LYS cc_start: 0.8102 (mttm) cc_final: 0.7206 (tmtt) REVERT: L 601 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7031 (tt) REVERT: M 36 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9041 (tp) REVERT: M 396 MET cc_start: 0.8411 (mmt) cc_final: 0.8129 (mmm) REVERT: N 11 MET cc_start: 0.8534 (mmp) cc_final: 0.7933 (mtp) REVERT: N 151 LEU cc_start: 0.8874 (tp) cc_final: 0.8601 (tp) REVERT: N 294 MET cc_start: 0.8504 (tpp) cc_final: 0.8223 (tpp) REVERT: V 126 MET cc_start: 0.7251 (mtt) cc_final: 0.6785 (mtt) REVERT: W 102 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: X 68 GLU cc_start: 0.6402 (pt0) cc_final: 0.5771 (tp30) REVERT: Y 64 GLN cc_start: 0.8442 (tt0) cc_final: 0.8203 (mt0) REVERT: Y 112 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: Y 141 TYR cc_start: 0.9233 (m-80) cc_final: 0.8981 (m-80) REVERT: Z 66 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: a 72 SER cc_start: 0.9113 (p) cc_final: 0.8819 (m) REVERT: a 74 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8182 (mtm-85) REVERT: c 112 LYS cc_start: 0.8832 (pttt) cc_final: 0.8586 (pttp) REVERT: d 100 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: d 140 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8020 (pptt) REVERT: d 290 THR cc_start: 0.8840 (t) cc_final: 0.8625 (m) REVERT: e 39 ARG cc_start: 0.8543 (mtt180) cc_final: 0.7754 (mtp-110) REVERT: e 59 ASP cc_start: 0.8608 (m-30) cc_final: 0.8408 (m-30) REVERT: e 74 LYS cc_start: 0.8188 (mttp) cc_final: 0.7897 (mmtt) REVERT: f 32 ASP cc_start: 0.9014 (t0) cc_final: 0.8771 (t0) REVERT: f 57 ILE cc_start: 0.8289 (mm) cc_final: 0.8036 (mm) REVERT: f 70 GLN cc_start: 0.8707 (pt0) cc_final: 0.8370 (pt0) REVERT: h 8 GLN cc_start: 0.9179 (tt0) cc_final: 0.8908 (mt0) REVERT: i 7 LEU cc_start: 0.8838 (mt) cc_final: 0.8358 (mp) REVERT: i 32 ASP cc_start: 0.8816 (t70) cc_final: 0.8427 (t0) REVERT: i 135 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8131 (mt0) REVERT: j 20 LYS cc_start: 0.8127 (tmmt) cc_final: 0.7909 (mttt) REVERT: j 29 LYS cc_start: 0.7758 (tttp) cc_final: 0.7158 (ttpp) REVERT: j 39 ASP cc_start: 0.7478 (m-30) cc_final: 0.7227 (t0) REVERT: j 82 ASP cc_start: 0.7397 (m-30) cc_final: 0.6791 (p0) REVERT: k 58 TYR cc_start: 0.8345 (t80) cc_final: 0.8133 (t80) REVERT: k 162 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7970 (mt-10) REVERT: k 185 LYS cc_start: 0.7617 (mtmp) cc_final: 0.7194 (tppt) REVERT: k 250 ASP cc_start: 0.8840 (p0) cc_final: 0.8499 (p0) REVERT: l 4 ASP cc_start: 0.8927 (t0) cc_final: 0.8684 (t0) REVERT: l 37 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8590 (tttm) REVERT: l 87 LYS cc_start: 0.6861 (mmtt) cc_final: 0.6118 (mmmt) REVERT: m 14 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7848 (mptt) REVERT: m 30 ILE cc_start: 0.8836 (pp) cc_final: 0.8532 (mt) REVERT: n 22 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7393 (mmmt) REVERT: p 52 ASP cc_start: 0.8116 (t0) cc_final: 0.7866 (t0) REVERT: p 65 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8607 (mp) REVERT: r 8 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7773 (tppt) REVERT: r 12 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8003 (mm-40) REVERT: r 98 GLU cc_start: 0.8536 (tt0) cc_final: 0.8269 (mt-10) REVERT: s 62 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8248 (tt) REVERT: t 10 THR cc_start: 0.7485 (p) cc_final: 0.7061 (p) REVERT: u 14 PHE cc_start: 0.7999 (t80) cc_final: 0.7541 (t80) REVERT: w 28 GLU cc_start: 0.7878 (tp30) cc_final: 0.7143 (pt0) REVERT: w 54 ASP cc_start: 0.8902 (t70) cc_final: 0.8381 (t0) REVERT: w 98 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7923 (tttp) REVERT: y 24 TYR cc_start: 0.8106 (t80) cc_final: 0.7787 (t80) REVERT: y 28 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.6903 (mtm110) outliers start: 205 outliers final: 172 residues processed: 1342 average time/residue: 0.6750 time to fit residues: 1536.7438 Evaluate side-chains 1386 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1200 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 49 LEU Chi-restraints excluded: chain 1 residue 172 ASP Chi-restraints excluded: chain 1 residue 228 VAL Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 174 ASP Chi-restraints excluded: chain 2 residue 181 ILE Chi-restraints excluded: chain 3 residue 196 SER Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 260 GLU Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 461 ASN Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 4 residue 68 LEU Chi-restraints excluded: chain 4 residue 77 ASP Chi-restraints excluded: chain 4 residue 240 VAL Chi-restraints excluded: chain 4 residue 246 THR Chi-restraints excluded: chain 4 residue 275 TYR Chi-restraints excluded: chain 4 residue 276 ASP Chi-restraints excluded: chain 4 residue 424 VAL Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 32 ILE Chi-restraints excluded: chain 5 residue 73 LYS Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 109 THR Chi-restraints excluded: chain 5 residue 112 ASP Chi-restraints excluded: chain 5 residue 178 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 126 CYS Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 121 TRP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 270 PHE Chi-restraints excluded: chain H residue 296 LEU Chi-restraints excluded: chain H residue 312 SER Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 148 SER Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain K residue 15 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 61 MET Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 86 SER Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 237 MET Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain L residue 401 THR Chi-restraints excluded: chain L residue 404 THR Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain L residue 509 HIS Chi-restraints excluded: chain L residue 525 LEU Chi-restraints excluded: chain L residue 543 THR Chi-restraints excluded: chain L residue 584 ILE Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain L residue 601 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 ASN Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 140 THR Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 214 LEU Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 274 SER Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 448 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 49 ASN Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 235 ASN Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain N residue 331 VAL Chi-restraints excluded: chain N residue 342 ILE Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 25 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 78 THR Chi-restraints excluded: chain W residue 102 GLU Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 48 VAL Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 22 SER Chi-restraints excluded: chain Y residue 62 VAL Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 79 GLU Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 132 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 66 GLU Chi-restraints excluded: chain Z residue 90 GLN Chi-restraints excluded: chain Z residue 144 ASP Chi-restraints excluded: chain Z residue 150 SER Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 67 SER Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 12 THR Chi-restraints excluded: chain b residue 20 ASP Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain c residue 31 LYS Chi-restraints excluded: chain c residue 87 SER Chi-restraints excluded: chain c residue 91 ASP Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain d residue 100 GLU Chi-restraints excluded: chain d residue 101 THR Chi-restraints excluded: chain d residue 156 VAL Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain d residue 222 ASP Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain f residue 16 CYS Chi-restraints excluded: chain f residue 103 VAL Chi-restraints excluded: chain g residue 47 HIS Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 72 CYS Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 86 VAL Chi-restraints excluded: chain k residue 6 LEU Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 71 VAL Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain l residue 37 LYS Chi-restraints excluded: chain l residue 57 ILE Chi-restraints excluded: chain l residue 92 THR Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 84 GLU Chi-restraints excluded: chain o residue 12 GLN Chi-restraints excluded: chain o residue 17 GLU Chi-restraints excluded: chain o residue 92 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain p residue 65 ILE Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 140 ILE Chi-restraints excluded: chain r residue 12 GLN Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain s residue 14 VAL Chi-restraints excluded: chain s residue 62 LEU Chi-restraints excluded: chain s residue 77 LEU Chi-restraints excluded: chain t residue 131 SER Chi-restraints excluded: chain t residue 140 GLN Chi-restraints excluded: chain t residue 143 THR Chi-restraints excluded: chain u residue 60 THR Chi-restraints excluded: chain v residue 31 VAL Chi-restraints excluded: chain v residue 81 LEU Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 102 CYS Chi-restraints excluded: chain v residue 115 MET Chi-restraints excluded: chain v residue 154 VAL Chi-restraints excluded: chain w residue 37 LEU Chi-restraints excluded: chain w residue 49 LYS Chi-restraints excluded: chain x residue 11 SER Chi-restraints excluded: chain x residue 16 LYS Chi-restraints excluded: chain z residue 48 MET Chi-restraints excluded: chain z residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 5.9990 chunk 500 optimal weight: 20.0000 chunk 671 optimal weight: 0.0050 chunk 193 optimal weight: 0.0970 chunk 581 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 631 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 648 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 overall best weight: 3.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 ASN 6 82 GLN ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN ** N 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN g 47 HIS ** h 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 180 GLN k 271 ASN n 58 ASN t 72 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106432 restraints weight = 103995.922| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.41 r_work: 0.3145 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68996 Z= 0.539 Angle : 1.570 50.620 93232 Z= 1.015 Chirality : 0.310 6.360 10101 Planarity : 0.004 0.076 11630 Dihedral : 10.872 171.740 10496 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.53 % Allowed : 14.30 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.48 (0.10), residues: 8036 helix: 1.09 (0.08), residues: 4228 sheet: -0.89 (0.25), residues: 399 loop : -0.43 (0.11), residues: 3409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP t 71 HIS 0.034 0.001 HIS g 47 PHE 0.031 0.001 PHE N 292 TYR 0.037 0.001 TYR d 145 ARG 0.015 0.000 ARG l 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23279.43 seconds wall clock time: 406 minutes 5.69 seconds (24365.69 seconds total)