Starting phenix.real_space_refine on Sat Feb 17 02:51:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v2e_31643/02_2024/7v2e_31643_updated.pdb" } resolution = 2.8 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= 0.007 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 Fe 28 7.16 5 Zn 1 6.06 5 P 47 5.49 5 Mg 1 5.21 5 S 483 5.16 5 C 44191 2.51 5 N 11249 2.21 5 O 12244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 211": "OE1" <-> "OE2" Residue "M GLU 535": "OE1" <-> "OE2" Residue "N PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 67": "OE1" <-> "OE2" Residue "O PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 209": "OE1" <-> "OE2" Residue "Q GLU 100": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 212": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "Q GLU 281": "OE1" <-> "OE2" Residue "Q GLU 336": "OE1" <-> "OE2" Residue "Q GLU 406": "OE1" <-> "OE2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "V GLU 138": "OE1" <-> "OE2" Residue "W TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 89": "OE1" <-> "OE2" Residue "W GLU 123": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "Y PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "a GLU 143": "OE1" <-> "OE2" Residue "a GLU 145": "OE1" <-> "OE2" Residue "b GLU 99": "OE1" <-> "OE2" Residue "c GLU 47": "OE1" <-> "OE2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "d GLU 119": "OE1" <-> "OE2" Residue "d PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 68": "OE1" <-> "OE2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "g GLU 101": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h GLU 42": "OE1" <-> "OE2" Residue "i GLU 117": "OE1" <-> "OE2" Residue "j GLU 112": "OE1" <-> "OE2" Residue "m GLU 77": "OE1" <-> "OE2" Residue "m GLU 81": "OE1" <-> "OE2" Residue "n GLU 48": "OE1" <-> "OE2" Residue "o GLU 35": "OE1" <-> "OE2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "p GLU 69": "OE1" <-> "OE2" Residue "p GLU 84": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s ARG 62": "NH1" <-> "NH2" Residue "s GLU 204": "OE1" <-> "OE2" Residue "s GLU 206": "OE1" <-> "OE2" Residue "w GLU 213": "OE1" <-> "OE2" Residue "w GLU 226": "OE1" <-> "OE2" Residue "w GLU 345": "OE1" <-> "OE2" 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: 68244 Number of models: 1 Model: "" Number of chains: 68 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3459 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 401} 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: "S" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 566 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 643 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 11, 'TRANS': 71} Chain: "V" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1021 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "W" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1167 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 584 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 6, 'TRANS': 60} Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "a" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1151 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 10, 'TRANS': 127} Chain: "b" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 819 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1315 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 20, 'TRANS': 135} Chain: "d" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1461 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 10, 'TRANS': 164} Chain: "e" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain: "f" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 378 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "g" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 11, 'TRANS': 109} Chain: "h" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 867 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "i" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2710 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 328} Chain: "j" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 914 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 748 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "l" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 577} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1295 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 171} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "n" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 479 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "o" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1062 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 11, 'TRANS': 116} Chain: "p" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1534 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 17, 'TRANS': 160} Chain: "r" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3631 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 438} Chain: "s" Number of atoms: 2508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2508 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 296} Chain: "u" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1398 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "v" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1059 Classifications: {'peptide': 124} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "w" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2582 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 303} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'PEE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'PEE': 1, 'PLX': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "J" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {' UQ': 1, 'NDP': 1, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 194 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "W" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "X" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 152 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "g" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PLX': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 144 Unusual residues: {'PEE': 2, 'PLX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "k" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 290 Unusual residues: {'CDL': 2, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 255 Unusual residues: {'CDL': 1, 'PEE': 1, 'PLX': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "s" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 127 Unusual residues: {' UQ': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 25 Chain: "w" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2718 SG CYS A 382 47.290 49.031 176.285 1.00 12.46 S ATOM 3060 SG CYS A 425 46.734 46.066 182.256 1.00 16.77 S ATOM 2738 SG CYS A 385 44.099 44.631 176.615 1.00 13.28 S ATOM 2699 SG CYS A 379 42.073 49.719 180.417 1.00 14.58 S ATOM 3961 SG CYS B 113 34.961 63.344 141.438 1.00 16.45 S ATOM 3980 SG CYS B 116 40.186 61.228 145.123 1.00 21.92 S ATOM 4003 SG CYS B 119 41.036 63.818 139.565 1.00 21.15 S ATOM 4332 SG CYS B 162 38.615 57.884 140.513 1.00 13.75 S ATOM 4030 SG CYS B 123 46.979 66.546 134.587 1.00 27.54 S ATOM 4256 SG CYS B 152 45.057 64.450 128.904 1.00 27.54 S ATOM 4303 SG CYS B 158 43.373 60.926 134.100 1.00 27.54 S ATOM 4282 SG CYS B 155 49.385 61.229 132.154 1.00 27.54 S ATOM 5724 SG CYS C 166 51.630 64.453 124.540 1.00 27.54 S ATOM 4996 SG CYS C 72 51.940 65.601 118.130 1.00 10.85 S ATOM 4990 SG CYS C 71 57.235 64.012 121.279 1.00 9.58 S ATOM 5494 SG CYS C 136 53.841 69.479 123.148 1.00 14.80 S ATOM 14949 SG CYS M 131 39.675 61.789 157.150 1.00 27.54 S ATOM 14928 SG CYS M 128 43.173 57.017 154.170 1.00 27.54 S ATOM 14989 SG CYS M 137 45.331 60.823 159.254 1.00 11.00 S ATOM 15321 SG CYS M 179 43.636 61.382 170.041 1.00 16.54 S ATOM 15675 SG CYS M 226 40.799 63.831 165.915 1.00 11.00 S ATOM 15345 SG CYS M 182 38.583 63.910 172.163 1.00 9.52 S ATOM 15298 SG CYS M 176 38.583 58.788 168.766 1.00 8.65 S ATOM 14546 SG CYS M 78 55.796 57.099 174.000 1.00 14.60 S ATOM 14647 SG CYS M 92 53.892 59.205 176.168 1.00 12.44 S ATOM 14435 SG CYS M 64 49.413 59.081 174.027 1.00 27.54 S ATOM 14521 SG CYS M 75 50.540 57.091 171.155 1.00 9.60 S ATOM 21484 SG CYS O 135 31.765 31.640 185.469 1.00 38.58 S ATOM 21518 SG CYS O 140 31.905 28.168 186.716 1.00 39.64 S ATOM 21798 SG CYS O 176 36.328 33.326 188.046 1.00 37.88 S ATOM 21821 SG CYS O 180 36.321 30.361 188.587 1.00 44.03 S ATOM 28560 SG CYS T 86 27.976 50.167 149.870 1.00 14.63 S ATOM 28738 SG CYS T 111 29.183 53.709 150.491 1.00 16.95 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' ADP w 401 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP w 401 " occ=0.50 Time building chain proxies: 26.39, per 1000 atoms: 0.39 Number of scatterers: 68244 At special positions: 0 Unit cell: (208.395, 216.988, 233.101, 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 S 483 16.00 P 47 15.00 Mg 1 11.99 O 12244 8.00 N 11249 7.00 C 44191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.05 Simple disulfide: pdb=" SG CYS V 18 " - pdb=" SG CYS V 75 " distance=2.03 Simple disulfide: pdb=" SG CYS V 95 " - pdb=" SG CYS V 115 " distance=2.03 Simple disulfide: pdb=" SG CYS d 113 " - pdb=" SG CYS d 125 " distance=2.03 Simple disulfide: pdb=" SG CYS h 33 " - pdb=" SG CYS h 66 " distance=2.03 Simple disulfide: pdb=" SG CYS u 46 " - pdb=" SG CYS u 56 " distance=2.03 Simple disulfide: pdb=" SG CYS u 78 " - pdb=" SG CYS u 110 " distance=2.03 Simple disulfide: pdb=" SG CYS u 88 " - pdb=" SG CYS u 100 " distance=2.03 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.10 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 353 helices and 30 sheets defined 52.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 95 through 102 removed outlier: 4.398A pdb=" N MET A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.536A pdb=" N VAL A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 363 through 377 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.360A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 419 Processing helix chain 'A' and resid 427 through 441 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 187 through 206 removed outlier: 5.636A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 60 Processing helix chain 'C' and resid 71 through 79 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 111 through 122 Proline residue: C 115 - end of helix Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'E' and resid 25 through 49 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 56 through 70 removed outlier: 4.269A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 106 removed outlier: 4.297A pdb=" N PHE E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 124 Processing helix chain 'F' and resid 28 through 47 removed outlier: 4.821A pdb=" N GLY F 32 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG F 40 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR F 41 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL F 42 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 43 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 84 through 95 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'G' and resid 112 through 126 Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'H' and resid 20 through 37 removed outlier: 4.164A pdb=" N GLN H 37 " --> pdb=" O ASP H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 60 Processing helix chain 'H' and resid 65 through 72 Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'I' and resid 6 through 16 Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' Processing helix chain 'I' and resid 54 through 56 No H-bonds generated for 'chain 'I' and resid 54 through 56' Processing helix chain 'I' and resid 59 through 62 Processing helix chain 'J' and resid 38 through 40 No H-bonds generated for 'chain 'J' and resid 38 through 40' Processing helix chain 'J' and resid 64 through 76 removed outlier: 4.188A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 97 removed outlier: 5.357A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 141 through 144 No H-bonds generated for 'chain 'J' and resid 141 through 144' Processing helix chain 'J' and resid 147 through 158 Processing helix chain 'J' and resid 179 through 194 Processing helix chain 'J' and resid 214 through 221 removed outlier: 3.574A pdb=" N MET J 220 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG J 221 " --> pdb=" O PHE J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 242 through 253 Processing helix chain 'J' and resid 273 through 283 Processing helix chain 'J' and resid 295 through 307 removed outlier: 3.970A pdb=" N VAL J 307 " --> pdb=" O ARG J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 335 through 338 Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 350 through 356 removed outlier: 5.588A pdb=" N ARG J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS J 356 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'K' and resid 77 through 80 removed outlier: 3.557A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 77 through 80' Processing helix chain 'K' and resid 85 through 95 removed outlier: 4.413A pdb=" N LYS K 95 " --> pdb=" O VAL K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.591A pdb=" N ILE L 72 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS L 73 " --> pdb=" O GLU L 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 73' Processing helix chain 'L' and resid 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' Processing helix chain 'L' and resid 131 through 141 Processing helix chain 'L' and resid 160 through 164 Processing helix chain 'M' and resid 49 through 56 removed outlier: 4.101A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 122 Processing helix chain 'M' and resid 128 through 130 No H-bonds generated for 'chain 'M' and resid 128 through 130' Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 219 through 225 removed outlier: 3.722A pdb=" N ILE M 222 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE M 225 " --> pdb=" O ILE M 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 292 Processing helix chain 'M' and resid 294 through 298 Processing helix chain 'M' and resid 319 through 332 removed outlier: 3.612A pdb=" N SER M 332 " --> pdb=" O GLY M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 337 No H-bonds generated for 'chain 'M' and resid 335 through 337' Processing helix chain 'M' and resid 348 through 360 Processing helix chain 'M' and resid 382 through 385 Processing helix chain 'M' and resid 392 through 396 removed outlier: 3.504A pdb=" N GLU M 395 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 410 No H-bonds generated for 'chain 'M' and resid 407 through 410' Processing helix chain 'M' and resid 412 through 424 Processing helix chain 'M' and resid 449 through 457 Processing helix chain 'M' and resid 461 through 468 Processing helix chain 'M' and resid 486 through 504 Processing helix chain 'M' and resid 522 through 528 Processing helix chain 'M' and resid 535 through 539 Processing helix chain 'M' and resid 619 through 630 Processing helix chain 'M' and resid 639 through 649 Processing helix chain 'M' and resid 651 through 653 No H-bonds generated for 'chain 'M' and resid 651 through 653' Processing helix chain 'M' and resid 665 through 672 Processing helix chain 'M' and resid 691 through 694 Processing helix chain 'M' and resid 699 through 703 Processing helix chain 'M' and resid 705 through 715 removed outlier: 3.529A pdb=" N LYS M 709 " --> pdb=" O GLN M 705 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 17 removed outlier: 3.607A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 29 Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.681A pdb=" N ASN O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 90 removed outlier: 4.542A pdb=" N LEU O 80 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Proline residue: O 81 - end of helix removed outlier: 3.591A pdb=" N ASN O 90 " --> pdb=" O GLN O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 105 Processing helix chain 'O' and resid 109 through 118 Processing helix chain 'O' and resid 138 through 142 Processing helix chain 'O' and resid 145 through 156 Processing helix chain 'O' and resid 198 through 208 Processing helix chain 'P' and resid 52 through 68 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.819A pdb=" N VAL P 93 " --> pdb=" O PRO P 90 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE P 94 " --> pdb=" O ASP P 91 " (cutoff:3.500A) Proline residue: P 95 - end of helix Processing helix chain 'P' and resid 161 through 174 removed outlier: 3.780A pdb=" N TRP P 165 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU P 167 " --> pdb=" O ASN P 164 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE P 174 " --> pdb=" O TRP P 171 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 245 No H-bonds generated for 'chain 'P' and resid 243 through 245' Processing helix chain 'Q' and resid 41 through 47 removed outlier: 4.060A pdb=" N GLN Q 46 " --> pdb=" O GLU Q 42 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE Q 47 " --> pdb=" O TRP Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 126 removed outlier: 3.580A pdb=" N TYR Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 139 removed outlier: 3.549A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 159 Processing helix chain 'Q' and resid 165 through 194 Processing helix chain 'Q' and resid 198 through 218 removed outlier: 3.649A pdb=" N TRP Q 202 " --> pdb=" O THR Q 198 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 262 removed outlier: 3.703A pdb=" N ASN Q 250 " --> pdb=" O GLU Q 246 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE Q 253 " --> pdb=" O LYS Q 249 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 272 Processing helix chain 'Q' and resid 280 through 285 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.505A pdb=" N GLY Q 295 " --> pdb=" O MET Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 302 through 305 No H-bonds generated for 'chain 'Q' and resid 302 through 305' Processing helix chain 'Q' and resid 311 through 313 No H-bonds generated for 'chain 'Q' and resid 311 through 313' Processing helix chain 'Q' and resid 326 through 349 Processing helix chain 'Q' and resid 368 through 371 No H-bonds generated for 'chain 'Q' and resid 368 through 371' Processing helix chain 'Q' and resid 375 through 386 Processing helix chain 'Q' and resid 427 through 433 Processing helix chain 'Q' and resid 435 through 438 No H-bonds generated for 'chain 'Q' and resid 435 through 438' Processing helix chain 'Q' and resid 444 through 453 Processing helix chain 'Q' and resid 458 through 462 Processing helix chain 'S' and resid 2 through 4 No H-bonds generated for 'chain 'S' and resid 2 through 4' Processing helix chain 'S' and resid 6 through 29 removed outlier: 3.666A pdb=" N ILE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Proline residue: S 19 - end of helix Processing helix chain 'S' and resid 42 through 55 Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'T' and resid 50 through 55 removed outlier: 3.553A pdb=" N ARG T 54 " --> pdb=" O ARG T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 91 through 93 No H-bonds generated for 'chain 'T' and resid 91 through 93' Processing helix chain 'U' and resid 4 through 15 Processing helix chain 'U' and resid 17 through 35 Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 79 through 82 No H-bonds generated for 'chain 'U' and resid 79 through 82' Processing helix chain 'V' and resid 4 through 10 Processing helix chain 'V' and resid 18 through 43 Processing helix chain 'V' and resid 49 through 80 Processing helix chain 'V' and resid 87 through 105 Processing helix chain 'V' and resid 108 through 131 Processing helix chain 'W' and resid 32 through 100 Proline residue: W 73 - end of helix removed outlier: 3.574A pdb=" N LYS W 99 " --> pdb=" O ALA W 95 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP W 100 " --> pdb=" O ILE W 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 137 Processing helix chain 'W' and resid 139 through 142 No H-bonds generated for 'chain 'W' and resid 139 through 142' Processing helix chain 'X' and resid 76 through 88 Processing helix chain 'X' and resid 112 through 126 Processing helix chain 'X' and resid 132 through 135 No H-bonds generated for 'chain 'X' and resid 132 through 135' Processing helix chain 'X' and resid 141 through 152 Processing helix chain 'Y' and resid 52 through 75 Processing helix chain 'Y' and resid 77 through 81 removed outlier: 3.522A pdb=" N LEU Y 81 " --> pdb=" O ASP Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 89 through 91 No H-bonds generated for 'chain 'Y' and resid 89 through 91' Processing helix chain 'Z' and resid 19 through 21 No H-bonds generated for 'chain 'Z' and resid 19 through 21' Processing helix chain 'Z' and resid 28 through 39 removed outlier: 4.005A pdb=" N ARG Z 39 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 54 removed outlier: 4.582A pdb=" N TRP Z 51 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG Z 52 " --> pdb=" O ASN Z 48 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR Z 53 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 63 through 67 Processing helix chain 'Z' and resid 71 through 87 Processing helix chain 'a' and resid 62 through 92 Proline residue: a 81 - end of helix Processing helix chain 'a' and resid 109 through 112 removed outlier: 3.593A pdb=" N TYR a 112 " --> pdb=" O HIS a 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 109 through 112' Processing helix chain 'a' and resid 116 through 125 Processing helix chain 'a' and resid 129 through 163 Processing helix chain 'a' and resid 176 through 178 No H-bonds generated for 'chain 'a' and resid 176 through 178' Processing helix chain 'b' and resid 6 through 25 Processing helix chain 'b' and resid 69 through 74 Processing helix chain 'b' and resid 76 through 88 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 45 through 54 Processing helix chain 'c' and resid 83 through 85 No H-bonds generated for 'chain 'c' and resid 83 through 85' Processing helix chain 'c' and resid 109 through 111 No H-bonds generated for 'chain 'c' and resid 109 through 111' Processing helix chain 'c' and resid 129 through 149 Processing helix chain 'd' and resid 29 through 58 removed outlier: 4.644A pdb=" N ARG d 43 " --> pdb=" O LEU d 39 " (cutoff:3.500A) Proline residue: d 44 - end of helix removed outlier: 3.579A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'd' and resid 82 through 116 Processing helix chain 'd' and resid 118 through 124 removed outlier: 3.862A pdb=" N TYR d 121 " --> pdb=" O GLY d 118 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ARG d 122 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN d 124 " --> pdb=" O TYR d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 143 Processing helix chain 'd' and resid 152 through 175 Processing helix chain 'e' and resid 66 through 69 No H-bonds generated for 'chain 'e' and resid 66 through 69' Processing helix chain 'e' and resid 80 through 94 Processing helix chain 'e' and resid 98 through 107 Processing helix chain 'e' and resid 116 through 132 Processing helix chain 'e' and resid 144 through 146 No H-bonds generated for 'chain 'e' and resid 144 through 146' Processing helix chain 'f' and resid 41 through 72 Processing helix chain 'g' and resid 18 through 22 removed outlier: 3.649A pdb=" N SER g 22 " --> pdb=" O GLU g 19 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 50 Processing helix chain 'g' and resid 60 through 98 removed outlier: 3.760A pdb=" N TYR g 76 " --> pdb=" O PHE g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 102 No H-bonds generated for 'chain 'g' and resid 100 through 102' Processing helix chain 'h' and resid 6 through 10 Processing helix chain 'h' and resid 16 through 18 No H-bonds generated for 'chain 'h' and resid 16 through 18' Processing helix chain 'h' and resid 26 through 28 No H-bonds generated for 'chain 'h' and resid 26 through 28' Processing helix chain 'h' and resid 34 through 44 Processing helix chain 'h' and resid 49 through 55 removed outlier: 4.203A pdb=" N LYS h 54 " --> pdb=" O ILE h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 57 through 68 Processing helix chain 'h' and resid 70 through 89 Processing helix chain 'h' and resid 96 through 98 No H-bonds generated for 'chain 'h' and resid 96 through 98' Processing helix chain 'i' and resid 3 through 22 Processing helix chain 'i' and resid 26 through 45 Proline residue: i 42 - end of helix removed outlier: 3.627A pdb=" N MET i 45 " --> pdb=" O ILE i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 80 Processing helix chain 'i' and resid 92 through 106 Processing helix chain 'i' and resid 112 through 121 Proline residue: i 116 - end of helix removed outlier: 3.546A pdb=" N THR i 119 " --> pdb=" O PRO i 116 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN i 120 " --> pdb=" O GLU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 144 removed outlier: 3.872A pdb=" N GLN i 134 " --> pdb=" O LEU i 130 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS i 135 " --> pdb=" O LEU i 131 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU i 136 " --> pdb=" O THR i 132 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA i 137 " --> pdb=" O TRP i 133 " (cutoff:3.500A) Proline residue: i 138 - end of helix Processing helix chain 'i' and resid 151 through 171 removed outlier: 3.672A pdb=" N LEU i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN i 171 " --> pdb=" O TRP i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 175 through 192 Processing helix chain 'i' and resid 198 through 221 Processing helix chain 'i' and resid 227 through 230 No H-bonds generated for 'chain 'i' and resid 227 through 230' Processing helix chain 'i' and resid 233 through 235 No H-bonds generated for 'chain 'i' and resid 233 through 235' Processing helix chain 'i' and resid 238 through 252 Processing helix chain 'i' and resid 258 through 272 Proline residue: i 262 - end of helix Processing helix chain 'i' and resid 277 through 300 removed outlier: 4.509A pdb=" N LEU i 288 " --> pdb=" O MET i 284 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN i 289 " --> pdb=" O THR i 285 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 316 Processing helix chain 'i' and resid 326 through 334 Processing helix chain 'i' and resid 337 through 346 Proline residue: i 341 - end of helix Processing helix chain 'j' and resid 2 through 23 Processing helix chain 'j' and resid 56 through 70 removed outlier: 3.631A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 73 through 80 Proline residue: j 76 - end of helix removed outlier: 3.784A pdb=" N SER j 79 " --> pdb=" O PRO j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 107 removed outlier: 3.607A pdb=" N LEU j 98 " --> pdb=" O LEU j 94 " (cutoff:3.500A) Processing helix chain 'k' and resid 3 through 20 Processing helix chain 'k' and resid 26 through 50 Processing helix chain 'k' and resid 55 through 85 removed outlier: 4.017A pdb=" N MET k 58 " --> pdb=" O LEU k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix 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 3 through 22 removed outlier: 3.562A pdb=" N LEU l 12 " --> pdb=" O THR l 8 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU l 15 " --> pdb=" O THR l 11 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR l 16 " --> pdb=" O LEU l 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE l 17 " --> pdb=" O THR l 13 " (cutoff:3.500A) Proline residue: l 18 - end of helix Processing helix chain 'l' and resid 32 through 57 removed outlier: 4.450A pdb=" N VAL l 49 " --> pdb=" O THR l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix Processing helix chain 'l' and resid 84 through 107 Proline residue: l 91 - end of helix removed outlier: 3.875A pdb=" N TRP l 106 " --> pdb=" O GLU l 102 " (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: 3.923A 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 224 Processing helix chain 'l' and resid 227 through 229 No H-bonds generated for 'chain 'l' and resid 227 through 229' Processing helix chain 'l' and resid 231 through 238 removed outlier: 3.620A pdb=" N SER l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET l 237 " --> pdb=" O LEU l 233 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU l 238 " --> pdb=" O PRO l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 241 through 246 Processing helix chain 'l' and resid 252 through 262 removed outlier: 4.401A pdb=" N GLY l 256 " --> pdb=" O VAL l 253 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 4.370A pdb=" N THR l 269 " --> pdb=" O PRO l 265 " (cutoff:3.500A) Processing helix chain 'l' and resid 271 through 294 removed outlier: 3.511A pdb=" N ILE l 293 " --> pdb=" O ALA l 289 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR l 294 " --> pdb=" O LEU l 290 " (cutoff:3.500A) Processing helix chain 'l' and resid 298 through 318 Processing helix chain 'l' and resid 322 through 349 removed outlier: 4.056A pdb=" N PHE l 334 " --> pdb=" O CYS l 330 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE l 335 " --> pdb=" O MET 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 367 through 380 Processing helix chain 'l' and resid 387 through 400 removed outlier: 4.064A pdb=" N SER l 391 " --> pdb=" O THR l 387 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU l 394 " --> pdb=" O TYR l 390 " (cutoff:3.500A) Processing helix chain 'l' and resid 406 through 431 removed outlier: 3.730A pdb=" N ALA l 420 " --> pdb=" O THR l 416 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE l 426 " --> pdb=" O TYR l 422 " (cutoff:3.500A) Processing helix chain 'l' and resid 448 through 469 removed outlier: 6.028A pdb=" N GLY l 465 " --> pdb=" O SER l 461 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N PHE l 466 " --> pdb=" O ILE 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: 3.727A pdb=" N THR l 508 " --> pdb=" O LEU l 504 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR l 509 " --> pdb=" O ASN l 505 " (cutoff:3.500A) Processing helix chain 'l' and resid 518 through 524 Processing helix chain 'l' and resid 526 through 533 Proline residue: l 530 - end of helix removed outlier: 4.132A pdb=" N MET l 533 " --> pdb=" O PRO l 530 " (cutoff:3.500A) Processing helix chain 'l' and resid 536 through 547 Processing helix chain 'l' and resid 557 through 561 Processing helix chain 'l' and resid 563 through 578 Processing helix chain 'l' and resid 584 through 600 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 26 through 45 Processing helix chain 'm' and resid 50 through 74 Processing helix chain 'm' and resid 87 through 108 Processing helix chain 'm' and resid 138 through 146 removed outlier: 4.113A pdb=" N LEU m 146 " --> pdb=" O GLY m 142 " (cutoff:3.500A) Processing helix chain 'm' and resid 151 through 172 Processing helix chain 'n' and resid 4 through 34 removed outlier: 6.307A pdb=" N VAL n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS n 14 " --> pdb=" O ASP n 10 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE n 15 " --> pdb=" O HIS n 11 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU n 16 " --> pdb=" O TRP n 12 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VAL n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) Proline residue: n 18 - end of helix removed outlier: 3.945A pdb=" N LYS n 34 " --> pdb=" O ARG n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 22 No H-bonds generated for 'chain 'o' and resid 20 through 22' Processing helix chain 'o' and resid 27 through 51 removed outlier: 3.851A pdb=" N GLN o 50 " --> pdb=" O GLU o 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 73 Processing helix chain 'o' and resid 77 through 79 No H-bonds generated for 'chain 'o' and resid 77 through 79' Processing helix chain 'o' and resid 84 through 118 Proline residue: o 97 - end of helix Processing helix chain 'p' and resid 12 through 30 Processing helix chain 'p' and resid 34 through 51 removed outlier: 4.761A pdb=" N HIS p 51 " --> pdb=" O ARG p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 74 Processing helix chain 'p' and resid 95 through 97 No H-bonds generated for 'chain 'p' and resid 95 through 97' Processing helix chain 'p' and resid 101 through 106 Processing helix chain 'p' and resid 109 through 113 Processing helix chain 'p' and resid 116 through 142 removed outlier: 4.838A pdb=" N GLU p 134 " --> pdb=" O ARG p 130 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARG p 135 " --> pdb=" O GLU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 168 through 171 No H-bonds generated for 'chain 'p' and resid 168 through 171' Processing helix chain 'r' and resid 2 through 17 Proline residue: r 7 - end of helix Proline residue: r 13 - end of helix Processing helix chain 'r' and resid 23 through 42 removed outlier: 4.192A pdb=" N SER r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU r 42 " --> pdb=" O SER r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 82 Proline residue: r 74 - end of helix removed outlier: 4.624A pdb=" N SER r 82 " --> pdb=" O MET r 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 89 through 111 removed outlier: 3.767A pdb=" N THR r 111 " --> pdb=" O ILE r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 136 removed outlier: 4.580A pdb=" N LEU r 126 " --> pdb=" O PHE r 122 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL r 127 " --> pdb=" O GLU r 123 " (cutoff:3.500A) Proline residue: r 128 - end of helix Processing helix chain 'r' and resid 142 through 171 removed outlier: 3.530A pdb=" N THR r 153 " --> pdb=" O PHE r 149 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY r 156 " --> pdb=" O TYR r 152 " (cutoff:3.500A) Proline residue: r 159 - end of helix Processing helix chain 'r' and resid 176 through 181 Processing helix chain 'r' and resid 190 through 206 removed outlier: 4.596A pdb=" N ALA r 202 " --> pdb=" O ALA r 198 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE r 203 " --> pdb=" O CYS r 199 " (cutoff:3.500A) Processing helix chain 'r' and resid 213 through 222 Proline residue: r 217 - end of helix removed outlier: 3.595A pdb=" N HIS r 220 " --> pdb=" O PRO r 217 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL r 221 " --> pdb=" O LYS r 218 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU r 222 " --> pdb=" O ALA r 219 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 233 Processing helix chain 'r' and resid 237 through 250 removed outlier: 5.220A pdb=" N THR r 248 " --> pdb=" O MET r 244 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ILE r 249 " --> pdb=" O ARG r 245 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU r 250 " --> pdb=" O ILE r 246 " (cutoff:3.500A) Processing helix chain 'r' and resid 253 through 278 removed outlier: 4.484A pdb=" N ALA r 258 " --> pdb=" O ASN r 255 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR r 259 " --> pdb=" O TYR r 256 " (cutoff:3.500A) Proline residue: r 260 - end of helix removed outlier: 3.638A pdb=" N TRP r 267 " --> pdb=" O LEU r 264 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY r 268 " --> pdb=" O SER r 265 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR r 272 " --> pdb=" O MET r 269 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS r 276 " --> pdb=" O SER r 273 " (cutoff:3.500A) Processing helix chain 'r' and resid 282 through 303 Processing helix chain 'r' and resid 306 through 337 removed outlier: 3.606A pdb=" N ASN r 333 " --> pdb=" O LEU r 329 " (cutoff:3.500A) Processing helix chain 'r' and resid 348 through 351 No H-bonds generated for 'chain 'r' and resid 348 through 351' Processing helix chain 'r' and resid 353 through 366 Processing helix chain 'r' and resid 373 through 388 Processing helix chain 'r' and resid 390 through 415 removed outlier: 3.906A pdb=" N ILE r 393 " --> pdb=" O ASN r 390 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA r 404 " --> pdb=" O MET r 401 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU r 408 " --> pdb=" O LEU r 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR r 414 " --> pdb=" O LEU r 411 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN r 415 " --> pdb=" O ILE r 412 " (cutoff:3.500A) Processing helix chain 'r' and resid 431 through 449 Proline residue: r 443 - end of helix Processing helix chain 'r' and resid 451 through 454 Processing helix chain 's' and resid 2 through 32 Proline residue: s 12 - end of helix removed outlier: 3.741A pdb=" N LEU s 22 " --> pdb=" O ALA s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 44 No H-bonds generated for 'chain 's' and resid 42 through 44' Processing helix chain 's' and resid 47 through 57 Processing helix chain 's' and resid 68 through 86 Proline residue: s 75 - end of helix removed outlier: 4.434A pdb=" N TRP s 86 " --> pdb=" O ALA s 82 " (cutoff:3.500A) Processing helix chain 's' and resid 101 through 122 removed outlier: 3.909A pdb=" N VAL s 113 " --> pdb=" O SER s 109 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR s 114 " --> pdb=" O SER s 110 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER s 115 " --> pdb=" O LEU s 111 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE s 116 " --> pdb=" O ALA s 112 " (cutoff:3.500A) Processing helix chain 's' and resid 126 through 156 removed outlier: 5.162A pdb=" N VAL s 144 " --> pdb=" O ILE s 140 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR s 145 " --> pdb=" O SER s 141 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET s 156 " --> pdb=" O SER s 152 " (cutoff:3.500A) Processing helix chain 's' and resid 163 through 168 removed outlier: 3.516A pdb=" N THR s 168 " --> pdb=" O LEU s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 176 No H-bonds generated for 'chain 's' and resid 174 through 176' Processing helix chain 's' and resid 179 through 192 Processing helix chain 's' and resid 204 through 207 No H-bonds generated for 'chain 's' and resid 204 through 207' Processing helix chain 's' and resid 210 through 212 No H-bonds generated for 'chain 's' and resid 210 through 212' Processing helix chain 's' and resid 217 through 242 Processing helix chain 's' and resid 252 through 276 Processing helix chain 's' and resid 282 through 291 Processing helix chain 's' and resid 293 through 311 Proline residue: s 308 - end of helix Processing helix chain 'u' and resid 10 through 13 Processing helix chain 'u' and resid 22 through 35 removed outlier: 4.837A pdb=" N HIS u 30 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS u 31 " --> pdb=" O ALA u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 50 Processing helix chain 'u' and resid 53 through 55 No H-bonds generated for 'chain 'u' and resid 53 through 55' Processing helix chain 'u' and resid 57 through 77 Processing helix chain 'u' and resid 80 through 91 Processing helix chain 'u' and resid 97 through 99 No H-bonds generated for 'chain 'u' and resid 97 through 99' Processing helix chain 'u' and resid 101 through 113 Processing helix chain 'v' and resid 3 through 10 Processing helix chain 'v' and resid 13 through 15 No H-bonds generated for 'chain 'v' and resid 13 through 15' Processing helix chain 'v' and resid 43 through 49 Processing helix chain 'v' and resid 60 through 72 Processing helix chain 'v' and resid 82 through 123 Processing helix chain 'w' and resid 40 through 44 Processing helix chain 'w' and resid 70 through 81 Processing helix chain 'w' and resid 93 through 97 removed outlier: 3.762A pdb=" N THR w 97 " --> pdb=" O TYR w 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 93 through 97' Processing helix chain 'w' and resid 114 through 119 Processing helix chain 'w' and resid 127 through 153 Processing helix chain 'w' and resid 166 through 175 removed outlier: 3.550A pdb=" N ARG w 175 " --> pdb=" O ALA w 172 " (cutoff:3.500A) Processing helix chain 'w' and resid 181 through 197 removed outlier: 4.131A pdb=" N CYS w 196 " --> pdb=" O LYS w 192 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU w 197 " --> pdb=" O VAL w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 211 through 221 Processing helix chain 'w' and resid 226 through 228 No H-bonds generated for 'chain 'w' and resid 226 through 228' Processing helix chain 'w' and resid 231 through 243 Processing helix chain 'w' and resid 245 through 251 removed outlier: 4.044A pdb=" N GLU w 251 " --> pdb=" O PRO w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 260 through 263 No H-bonds generated for 'chain 'w' and resid 260 through 263' Processing helix chain 'w' and resid 266 through 273 Processing helix chain 'w' and resid 283 through 285 No H-bonds generated for 'chain 'w' and resid 283 through 285' Processing helix chain 'w' and resid 288 through 298 Processing helix chain 'w' and resid 301 through 309 removed outlier: 5.071A pdb=" N TYR w 307 " --> pdb=" O GLU w 303 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR w 308 " --> pdb=" O VAL w 304 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR w 309 " --> pdb=" O LEU w 305 " (cutoff:3.500A) Processing helix chain 'w' and resid 321 through 332 Processing helix chain 'w' and resid 345 through 347 No H-bonds generated for 'chain 'w' and resid 345 through 347' Processing helix chain 'w' and resid 352 through 354 No H-bonds generated for 'chain 'w' and resid 352 through 354' Processing sheet with id= A, first strand: chain 'A' and resid 240 through 244 removed outlier: 7.372A pdb=" N TYR A 112 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N ALA A 243 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 114 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA A 153 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL A 115 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR A 155 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA A 117 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR A 157 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ASP A 194 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 156 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE A 196 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE A 158 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 198 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 286 through 291 Processing sheet with id= C, first strand: chain 'B' and resid 99 through 103 removed outlier: 4.372A pdb=" N HIS B 101 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 168 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 128 through 134 removed outlier: 5.870A pdb=" N GLU B 133 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR B 142 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.472A pdb=" N TYR C 129 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL C 105 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C 131 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 161 " --> pdb=" O SER C 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 52 through 58 removed outlier: 6.686A pdb=" N ARG F 68 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE F 19 " --> pdb=" O TRP F 66 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP F 66 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE F 21 " --> pdb=" O LYS F 64 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS F 64 " --> pdb=" O ILE F 21 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 262 through 265 removed outlier: 6.627A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE J 167 " --> pdb=" O ASN J 128 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN J 79 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL J 58 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE J 81 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 226 through 229 Processing sheet with id= I, first strand: chain 'L' and resid 144 through 147 Processing sheet with id= J, first strand: chain 'L' and resid 106 through 108 Processing sheet with id= K, first strand: chain 'M' and resid 32 through 36 Processing sheet with id= L, first strand: chain 'M' and resid 79 through 81 Processing sheet with id= M, first strand: chain 'M' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'M' and resid 196 through 200 removed outlier: 3.735A pdb=" N ARG M 200 " --> pdb=" O ASP M 203 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 246 through 251 removed outlier: 3.592A pdb=" N ARG M 272 " --> pdb=" O SER M 264 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= Q, first strand: chain 'M' and resid 365 through 368 removed outlier: 4.571A pdb=" N SER M 365 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL M 544 " --> pdb=" O ALA M 339 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE M 341 " --> pdb=" O VAL M 544 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE M 546 " --> pdb=" O ILE M 341 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE M 565 " --> pdb=" O LEU M 545 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU M 547 " --> pdb=" O PHE M 565 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE M 567 " --> pdb=" O LEU M 547 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL M 582 " --> pdb=" O TYR M 568 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLY M 570 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU M 584 " --> pdb=" O GLY M 570 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'M' and resid 513 through 516 removed outlier: 8.097A pdb=" N ASN M 514 " --> pdb=" O PRO M 472 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS M 428 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU M 402 " --> pdb=" O LYS M 428 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA M 430 " --> pdb=" O LEU M 402 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP M 443 " --> pdb=" O LEU M 431 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 595 through 597 Processing sheet with id= T, first strand: chain 'N' and resid 60 through 63 removed outlier: 6.670A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.640A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 110 through 118 removed outlier: 6.707A pdb=" N ASN P 131 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU P 114 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL P 129 " --> pdb=" O LEU P 114 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA P 116 " --> pdb=" O GLU P 127 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU P 127 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 208 through 213 Processing sheet with id= X, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.410A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id= Z, first strand: chain 'T' and resid 77 through 79 Processing sheet with id= AA, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= AB, first strand: chain 'l' and resid 62 through 67 removed outlier: 6.730A pdb=" N LEU l 78 " --> pdb=" O ASN l 65 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'w' and resid 60 through 64 removed outlier: 6.643A pdb=" N VAL w 203 " --> pdb=" O THR w 61 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP w 63 " --> pdb=" O VAL w 203 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL w 205 " --> pdb=" O ASP w 63 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU w 254 " --> pdb=" O VAL w 204 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR w 206 " --> pdb=" O GLU w 254 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU w 256 " --> pdb=" O TYR w 206 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP w 208 " --> pdb=" O LEU w 256 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR w 258 " --> pdb=" O ASP w 208 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'w' and resid 84 through 86 2898 hydrogen bonds defined for protein. 8121 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: 21.83 Time building geometry restraints manager: 24.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 27717 1.40 - 1.62: 41269 1.62 - 1.84: 859 1.84 - 2.06: 6 2.06 - 2.28: 80 Bond restraints: 69931 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.261 0.263 2.00e-02 2.50e+03 1.73e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.285 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.632 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.297 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3' ADP w 401 " pdb=" C4' ADP w 401 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 69926 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.93: 76 85.93 - 98.31: 5 98.31 - 110.70: 22635 110.70 - 123.08: 68151 123.08 - 135.46: 3652 Bond angle restraints: 94519 Sorted by residual: angle pdb=" N TYR I 28 " pdb=" CA TYR I 28 " pdb=" C TYR I 28 " ideal model delta sigma weight residual 111.14 119.98 -8.84 1.08e+00 8.57e-01 6.69e+01 angle pdb=" N GLU s 206 " pdb=" CA GLU s 206 " pdb=" C GLU s 206 " ideal model delta sigma weight residual 111.36 120.15 -8.79 1.09e+00 8.42e-01 6.50e+01 angle pdb=" N ASN M 74 " pdb=" CA ASN M 74 " pdb=" C ASN M 74 " ideal model delta sigma weight residual 111.36 120.12 -8.76 1.09e+00 8.42e-01 6.46e+01 angle pdb=" N VAL s 39 " pdb=" CA VAL s 39 " pdb=" C VAL s 39 " ideal model delta sigma weight residual 110.72 118.52 -7.80 1.01e+00 9.80e-01 5.96e+01 angle pdb=" C11 CDL V 201 " pdb=" CA5 CDL V 201 " pdb=" OA6 CDL V 201 " ideal model delta sigma weight residual 111.33 120.57 -9.24 1.32e+00 5.72e-01 4.89e+01 ... (remaining 94514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 41218 34.56 - 69.12: 1258 69.12 - 103.69: 125 103.69 - 138.25: 20 138.25 - 172.81: 16 Dihedral angle restraints: 42637 sinusoidal: 18546 harmonic: 24091 Sorted by residual: dihedral pdb=" C5' ADP w 401 " pdb=" O5' ADP w 401 " pdb=" PA ADP w 401 " pdb=" O2A ADP w 401 " ideal model delta sinusoidal sigma weight residual 300.00 129.94 170.06 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C10 FMN A 502 " pdb=" C1' FMN A 502 " pdb=" N10 FMN A 502 " pdb=" C2' FMN A 502 " ideal model delta sinusoidal sigma weight residual -102.41 54.60 -157.01 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" CA ALA A 186 " pdb=" C ALA A 186 " pdb=" N CYS A 187 " pdb=" CA CYS A 187 " ideal model delta harmonic sigma weight residual -180.00 -146.35 -33.65 0 5.00e+00 4.00e-02 4.53e+01 ... (remaining 42634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 9536 0.097 - 0.194: 575 0.194 - 0.291: 58 0.291 - 0.388: 16 0.388 - 0.485: 6 Chirality restraints: 10191 Sorted by residual: chirality pdb=" CA HIS r 422 " pdb=" N HIS r 422 " pdb=" C HIS r 422 " pdb=" CB HIS r 422 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CA MET M 173 " pdb=" N MET M 173 " pdb=" C MET M 173 " pdb=" CB MET M 173 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA PHE P 198 " pdb=" N PHE P 198 " pdb=" C PHE P 198 " pdb=" CB PHE P 198 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 10188 not shown) Planarity restraints: 11777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 UQ s 402 " 0.358 2.00e-02 2.50e+03 3.30e-01 1.36e+03 pdb=" C18 UQ s 402 " -0.349 2.00e-02 2.50e+03 pdb=" C19 UQ s 402 " -0.390 2.00e-02 2.50e+03 pdb=" C20 UQ s 402 " 0.005 2.00e-02 2.50e+03 pdb=" C21 UQ s 402 " 0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 402 " -0.008 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C11 UQ J 402 " -0.028 2.00e-02 2.50e+03 pdb=" C7 UQ J 402 " -0.304 2.00e-02 2.50e+03 pdb=" C8 UQ J 402 " 0.573 2.00e-02 2.50e+03 pdb=" C9 UQ J 402 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 402 " -0.315 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C13 UQ J 402 " 0.278 2.00e-02 2.50e+03 pdb=" C14 UQ J 402 " 0.389 2.00e-02 2.50e+03 pdb=" C15 UQ J 402 " -0.002 2.00e-02 2.50e+03 pdb=" C16 UQ J 402 " -0.350 2.00e-02 2.50e+03 ... (remaining 11774 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 122 2.34 - 2.98: 32811 2.98 - 3.62: 101661 3.62 - 4.26: 169267 4.26 - 4.90: 279720 Nonbonded interactions: 583581 Sorted by model distance: nonbonded pdb=" OG SER L 122 " pdb=" OE2 GLU P 229 " model vdw 1.695 2.440 nonbonded pdb=" NE2 GLN Q 36 " pdb=" O GLY r 137 " model vdw 1.703 2.520 nonbonded pdb=" N SER G 112 " pdb=" O1 8Q1 G 201 " model vdw 1.753 2.496 nonbonded pdb=" O LEU M 351 " pdb=" OH TYR M 530 " model vdw 1.899 2.440 nonbonded pdb=" OH TYR M 385 " pdb=" OD1 ASP M 527 " model vdw 1.903 2.440 ... (remaining 583576 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 'G' and (resid 69 through 93 or (resid 94 and (name N or name CA or name \ C or name O or name CB )) or resid 95 through 156 or resid 201)) selection = (chain 'X' and (resid 69 through 149 or (resid 150 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 156 or resid 201)) } 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=0.50 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 9.210 Check model and map are aligned: 0.790 Set scattering table: 0.520 Process input model: 158.410 Find NCS groups from input model: 2.120 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:10.620 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.008 0.263 69931 Z= 0.500 Angle : 0.901 17.333 94519 Z= 0.496 Chirality : 0.053 0.485 10191 Planarity : 0.008 0.330 11777 Dihedral : 16.492 172.809 27083 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.63 % Favored : 96.15 % Rotamer: Outliers : 0.40 % Allowed : 0.95 % Favored : 98.65 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.73 (0.09), residues: 8172 helix: 1.39 (0.08), residues: 4274 sheet: 0.04 (0.25), residues: 414 loop : -0.57 (0.10), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.001 TRP J 108 HIS 0.014 0.001 HIS S 27 PHE 0.034 0.002 PHE s 270 TYR 0.070 0.002 TYR C 142 ARG 0.006 0.000 ARG W 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1326 time to evaluate : 6.204 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 451 GLN cc_start: 0.7902 (pt0) cc_final: 0.7435 (pt0) REVERT: C 58 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7908 (mtt180) REVERT: E 68 MET cc_start: 0.8660 (mmm) cc_final: 0.8284 (mmm) REVERT: F 35 ASP cc_start: 0.7797 (m-30) cc_final: 0.7507 (m-30) REVERT: K 90 ASN cc_start: 0.9112 (t0) cc_final: 0.8788 (t0) REVERT: M 320 GLU cc_start: 0.7573 (mp0) cc_final: 0.7309 (mp0) REVERT: M 437 ASP cc_start: 0.8452 (t0) cc_final: 0.8241 (t0) REVERT: M 468 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: M 470 LYS cc_start: 0.8679 (mptt) cc_final: 0.8306 (mmmt) REVERT: U 62 ASN cc_start: 0.7804 (m110) cc_final: 0.7529 (m110) REVERT: V 141 VAL cc_start: 0.8629 (t) cc_final: 0.8384 (m) REVERT: X 111 ASP cc_start: 0.7920 (p0) cc_final: 0.7708 (p0) REVERT: X 124 ASP cc_start: 0.8252 (m-30) cc_final: 0.8040 (m-30) REVERT: b 108 ASP cc_start: 0.7794 (m-30) cc_final: 0.7587 (m-30) REVERT: f 61 GLN cc_start: 0.8091 (tp40) cc_final: 0.7811 (tp40) REVERT: g 109 LYS cc_start: 0.8479 (mmmm) cc_final: 0.8264 (mmmm) REVERT: h 99 LEU cc_start: 0.8118 (mp) cc_final: 0.7835 (mp) REVERT: i 177 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8745 (mttt) REVERT: j 83 ASN cc_start: 0.8845 (p0) cc_final: 0.8592 (p0) REVERT: l 119 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8902 (ttpt) REVERT: l 129 MET cc_start: 0.8233 (mmp) cc_final: 0.7857 (mmp) REVERT: m 1 MET cc_start: 0.3775 (mtt) cc_final: 0.1428 (tmm) REVERT: m 11 THR cc_start: 0.9224 (m) cc_final: 0.8993 (m) REVERT: r 229 MET cc_start: 0.9266 (mtp) cc_final: 0.9038 (mtp) REVERT: s 61 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7741 (mm) REVERT: u 44 MET cc_start: 0.8881 (mmm) cc_final: 0.8500 (mmm) outliers start: 29 outliers final: 10 residues processed: 1347 average time/residue: 1.6096 time to fit residues: 2773.9601 Evaluate side-chains 1124 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1110 time to evaluate : 6.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain d residue 64 TYR Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain l residue 119 LYS Chi-restraints excluded: chain l residue 320 ASN Chi-restraints excluded: chain l residue 423 SER Chi-restraints excluded: chain l residue 492 ILE Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 61 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 679 optimal weight: 6.9990 chunk 610 optimal weight: 1.9990 chunk 338 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 411 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 630 optimal weight: 0.0870 chunk 244 optimal weight: 8.9990 chunk 383 optimal weight: 3.9990 chunk 469 optimal weight: 1.9990 chunk 731 optimal weight: 0.8980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN J 138 ASN ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 514 ASN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 116 ASN O 69 ASN P 63 GLN S 31 ASN U 52 ASN U 71 GLN Z 33 GLN Z 60 ASN c 164 ASN d 107 GLN d 140 GLN e 115 GLN h 45 HIS h 98 HIS i 171 ASN i 273 ASN i 319 HIS k 50 ASN l 25 ASN l 72 GLN l 351 ASN l 479 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 51 ASN r 139 GLN ** r 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN v 110 GLN w 107 GLN w 322 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 69931 Z= 0.178 Angle : 0.559 13.485 94519 Z= 0.282 Chirality : 0.041 0.182 10191 Planarity : 0.005 0.071 11777 Dihedral : 15.569 172.610 10886 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 9.20 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.84 (0.09), residues: 8172 helix: 1.50 (0.08), residues: 4281 sheet: 0.18 (0.25), residues: 416 loop : -0.56 (0.11), residues: 3475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.010 0.001 HIS S 27 PHE 0.029 0.001 PHE i 292 TYR 0.038 0.001 TYR C 142 ARG 0.006 0.000 ARG k 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1159 time to evaluate : 6.244 Fit side-chains TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8277 (tp30) REVERT: A 208 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7016 (tm-30) REVERT: C 154 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8030 (p0) REVERT: E 68 MET cc_start: 0.8683 (mmm) cc_final: 0.8308 (mmm) REVERT: E 110 THR cc_start: 0.8386 (p) cc_final: 0.8171 (m) REVERT: F 95 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7463 (mt) REVERT: H 73 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: K 90 ASN cc_start: 0.9117 (t0) cc_final: 0.8741 (t0) REVERT: M 437 ASP cc_start: 0.8512 (t0) cc_final: 0.8291 (t0) REVERT: M 468 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: M 470 LYS cc_start: 0.8585 (mptt) cc_final: 0.8317 (mmmt) REVERT: M 628 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: M 688 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: O 215 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8119 (mttp) REVERT: U 62 ASN cc_start: 0.7723 (m110) cc_final: 0.7425 (m110) REVERT: W 98 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7699 (mmm) REVERT: X 123 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7849 (mt-10) REVERT: b 108 ASP cc_start: 0.7794 (m-30) cc_final: 0.7580 (m-30) REVERT: c 43 LYS cc_start: 0.7937 (mtmp) cc_final: 0.7535 (mtmm) REVERT: d 79 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: e 130 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: g 109 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8253 (mmmm) REVERT: i 104 MET cc_start: 0.8483 (ttm) cc_final: 0.8155 (ttm) REVERT: j 44 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7400 (ttt) REVERT: j 83 ASN cc_start: 0.8768 (p0) cc_final: 0.8563 (p0) REVERT: l 129 MET cc_start: 0.8243 (mmp) cc_final: 0.7943 (mmp) REVERT: l 176 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8119 (tpt90) REVERT: m 1 MET cc_start: 0.3648 (mtt) cc_final: 0.1153 (tmm) REVERT: m 173 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7959 (ttm-80) REVERT: p 66 GLN cc_start: 0.7598 (mp10) cc_final: 0.7332 (mp10) REVERT: r 229 MET cc_start: 0.9284 (mtp) cc_final: 0.9004 (mtp) REVERT: s 61 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7842 (mm) REVERT: s 156 MET cc_start: 0.8112 (mmp) cc_final: 0.7836 (mmt) REVERT: s 222 MET cc_start: 0.8878 (mtp) cc_final: 0.8565 (mtp) REVERT: s 227 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: u 44 MET cc_start: 0.8947 (mmm) cc_final: 0.8585 (mmm) REVERT: u 155 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7474 (pp20) REVERT: v 39 MET cc_start: 0.7995 (tpt) cc_final: 0.7762 (tpp) REVERT: v 70 LYS cc_start: 0.8661 (mtpm) cc_final: 0.8256 (mtpt) REVERT: v 105 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: w 238 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7053 (tp30) outliers start: 139 outliers final: 50 residues processed: 1218 average time/residue: 1.6019 time to fit residues: 2507.5230 Evaluate side-chains 1175 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1106 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 73 GLN Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 712 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 201 ASP Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 79 GLU Chi-restraints excluded: chain e residue 130 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 238 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 406 optimal weight: 7.9990 chunk 226 optimal weight: 10.0000 chunk 608 optimal weight: 7.9990 chunk 497 optimal weight: 8.9990 chunk 201 optimal weight: 6.9990 chunk 732 optimal weight: 0.5980 chunk 791 optimal weight: 2.9990 chunk 652 optimal weight: 3.9990 chunk 726 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 587 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 HIS H 50 GLN I 51 ASN J 72 HIS ** K 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 113 HIS N 116 ASN O 48 ASN P 63 GLN Q 88 HIS Q 190 HIS Z 33 GLN c 164 ASN c 183 HIS e 115 GLN f 61 GLN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS k 50 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN l 479 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 51 ASN r 139 GLN s 304 HIS u 77 HIS v 54 GLN v 110 GLN w 107 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 69931 Z= 0.331 Angle : 0.620 11.388 94519 Z= 0.313 Chirality : 0.045 0.208 10191 Planarity : 0.005 0.060 11777 Dihedral : 14.761 175.108 10869 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.50 % Allowed : 10.79 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.57 (0.09), residues: 8172 helix: 1.28 (0.08), residues: 4280 sheet: -0.07 (0.24), residues: 419 loop : -0.66 (0.10), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.014 0.001 HIS l 534 PHE 0.029 0.002 PHE s 270 TYR 0.039 0.002 TYR C 142 ARG 0.006 0.001 ARG n 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1315 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1136 time to evaluate : 6.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 MET cc_start: 0.8271 (mmm) cc_final: 0.8057 (mmm) REVERT: B 200 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: C 154 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8084 (p0) REVERT: F 95 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7381 (mt) REVERT: J 341 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.6977 (mp10) REVERT: K 90 ASN cc_start: 0.9074 (t0) cc_final: 0.8745 (t0) REVERT: M 150 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8248 (mtp85) REVERT: M 468 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: M 470 LYS cc_start: 0.8636 (mptt) cc_final: 0.8383 (mmmt) REVERT: M 628 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: M 688 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8020 (mt0) REVERT: O 160 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8329 (t) REVERT: O 215 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: T 43 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8869 (tm-30) REVERT: X 123 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8114 (mt-10) REVERT: Z 49 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: Z 79 VAL cc_start: 0.8798 (p) cc_final: 0.8550 (m) REVERT: c 43 LYS cc_start: 0.7941 (mtmp) cc_final: 0.7575 (mtmm) REVERT: c 143 MET cc_start: 0.8445 (mmm) cc_final: 0.8201 (mmm) REVERT: d 134 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6811 (mp10) REVERT: e 127 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8463 (ttpt) REVERT: e 130 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: f 61 GLN cc_start: 0.8592 (tp40) cc_final: 0.8024 (tp40) REVERT: h 102 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7315 (pt0) REVERT: i 68 MET cc_start: 0.8754 (mmp) cc_final: 0.8521 (mmp) REVERT: l 129 MET cc_start: 0.8162 (mmp) cc_final: 0.7872 (mmp) REVERT: l 176 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8208 (tpt90) REVERT: l 383 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7576 (tpt) REVERT: m 1 MET cc_start: 0.3866 (mtt) cc_final: 0.1406 (tmm) REVERT: r 243 MET cc_start: 0.8560 (mmm) cc_final: 0.8226 (tpp) REVERT: s 61 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8160 (mm) REVERT: s 227 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: u 155 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: v 39 MET cc_start: 0.8109 (tpt) cc_final: 0.7869 (tpp) REVERT: v 48 ASP cc_start: 0.7703 (m-30) cc_final: 0.7390 (m-30) REVERT: v 70 LYS cc_start: 0.8720 (mtpm) cc_final: 0.8323 (mtpt) REVERT: v 105 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: w 95 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: w 267 GLU cc_start: 0.7165 (tp30) cc_final: 0.6946 (tp30) outliers start: 179 outliers final: 88 residues processed: 1224 average time/residue: 1.6277 time to fit residues: 2560.3968 Evaluate side-chains 1205 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1094 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 374 THR Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 712 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 160 VAL Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 138 GLU Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 114 LYS Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain e residue 130 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 383 MET Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 14 GLN Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain s residue 311 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 723 optimal weight: 0.9990 chunk 550 optimal weight: 8.9990 chunk 380 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 349 optimal weight: 5.9990 chunk 491 optimal weight: 9.9990 chunk 734 optimal weight: 0.4980 chunk 778 optimal weight: 4.9990 chunk 383 optimal weight: 5.9990 chunk 696 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN K 78 HIS K 106 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 666 GLN N 52 ASN N 116 ASN O 48 ASN O 153 GLN P 63 GLN U 11 ASN Z 33 GLN c 164 ASN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS k 50 ASN l 323 HIS l 351 ASN l 479 ASN ** l 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 43 ASN r 51 ASN r 139 GLN r 279 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 69931 Z= 0.368 Angle : 0.625 11.274 94519 Z= 0.318 Chirality : 0.046 0.205 10191 Planarity : 0.005 0.065 11777 Dihedral : 14.450 176.132 10867 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 2.99 % Allowed : 11.68 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.43 (0.09), residues: 8172 helix: 1.15 (0.08), residues: 4276 sheet: -0.11 (0.25), residues: 402 loop : -0.71 (0.10), residues: 3494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP u 86 HIS 0.014 0.001 HIS S 27 PHE 0.028 0.002 PHE i 292 TYR 0.023 0.002 TYR C 142 ARG 0.008 0.001 ARG J 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1116 time to evaluate : 6.274 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ARG cc_start: 0.8518 (mtp180) cc_final: 0.8313 (mtt180) REVERT: C 192 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9100 (mt) REVERT: E 23 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7590 (mtt-85) REVERT: E 30 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7814 (ttm110) REVERT: F 38 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: F 57 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7377 (tp30) REVERT: F 95 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7460 (mt) REVERT: J 234 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: J 341 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: K 75 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7936 (t0) REVERT: K 90 ASN cc_start: 0.9072 (t0) cc_final: 0.8740 (t0) REVERT: M 150 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8167 (mtp85) REVERT: M 213 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6066 (mmt) REVERT: M 468 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: M 470 LYS cc_start: 0.8639 (mptt) cc_final: 0.8314 (mmmt) REVERT: M 628 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: M 688 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: N 12 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: O 215 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8161 (mttp) REVERT: T 43 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8884 (tm-30) REVERT: V 51 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6934 (mt-10) REVERT: W 98 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7823 (mmm) REVERT: W 100 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6180 (t0) REVERT: X 123 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8088 (mt-10) REVERT: Z 49 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: a 188 ASP cc_start: 0.8566 (m-30) cc_final: 0.8360 (m-30) REVERT: c 43 LYS cc_start: 0.7958 (mtmp) cc_final: 0.7581 (mtmm) REVERT: c 143 MET cc_start: 0.8390 (mmm) cc_final: 0.8116 (mmm) REVERT: d 79 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: d 134 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6851 (mp10) REVERT: e 127 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8475 (ttpt) REVERT: e 130 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: f 61 GLN cc_start: 0.8569 (tp40) cc_final: 0.7970 (tp40) REVERT: h 102 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7193 (pt0) REVERT: l 176 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8254 (tpt90) REVERT: l 271 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7964 (mttt) REVERT: l 411 MET cc_start: 0.8095 (mmp) cc_final: 0.7720 (mmp) REVERT: m 46 ASN cc_start: 0.8821 (m-40) cc_final: 0.8572 (m110) REVERT: o 106 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8163 (tmtt) REVERT: p 152 GLU cc_start: 0.7107 (pt0) cc_final: 0.6896 (pt0) REVERT: r 103 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: r 243 MET cc_start: 0.8527 (mmm) cc_final: 0.8159 (tpp) REVERT: s 61 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8267 (mm) REVERT: s 227 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: u 6 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6460 (tm-30) REVERT: u 155 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: v 39 MET cc_start: 0.8166 (tpt) cc_final: 0.7931 (tpp) REVERT: v 48 ASP cc_start: 0.7717 (m-30) cc_final: 0.7417 (m-30) REVERT: v 70 LYS cc_start: 0.8738 (mtpm) cc_final: 0.8400 (mtpt) REVERT: v 105 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: w 95 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: w 267 GLU cc_start: 0.7114 (tp30) cc_final: 0.6844 (tp30) outliers start: 214 outliers final: 102 residues processed: 1227 average time/residue: 1.5979 time to fit residues: 2523.5762 Evaluate side-chains 1228 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1092 time to evaluate : 6.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 75 ASN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 369 GLU Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 459 ASN Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 712 LYS Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain W residue 98 MET Chi-restraints excluded: chain W residue 100 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 46 THR Chi-restraints excluded: chain d residue 79 GLU Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain e residue 130 GLU Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 102 GLU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 19 LEU Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 186 MET Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 302 VAL Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 106 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 234 MET Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain s residue 311 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain u residue 162 LYS Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain v residue 105 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 648 optimal weight: 0.8980 chunk 441 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 579 optimal weight: 3.9990 chunk 321 optimal weight: 0.0040 chunk 664 optimal weight: 4.9990 chunk 537 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 397 optimal weight: 3.9990 chunk 698 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN F 31 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 112 ASN N 116 ASN P 63 GLN U 11 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 GLN Z 33 GLN c 164 ASN i 171 ASN i 319 HIS k 50 ASN l 351 ASN l 479 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 51 ASN r 139 GLN v 54 GLN w 107 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 69931 Z= 0.181 Angle : 0.538 10.600 94519 Z= 0.273 Chirality : 0.041 0.189 10191 Planarity : 0.005 0.062 11777 Dihedral : 13.884 177.297 10867 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 2.48 % Allowed : 12.92 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.71 (0.09), residues: 8172 helix: 1.40 (0.08), residues: 4298 sheet: -0.15 (0.24), residues: 429 loop : -0.60 (0.10), residues: 3445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.029 0.001 PHE i 292 TYR 0.021 0.001 TYR r 406 ARG 0.007 0.000 ARG g 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1132 time to evaluate : 6.286 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 THR cc_start: 0.8504 (t) cc_final: 0.8271 (t) REVERT: A 387 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: C 154 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8033 (p0) REVERT: C 192 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9058 (mt) REVERT: E 23 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7554 (mtt-85) REVERT: E 110 THR cc_start: 0.8426 (p) cc_final: 0.8176 (m) REVERT: F 57 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: F 95 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7395 (mt) REVERT: J 234 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: J 341 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6970 (mp10) REVERT: K 90 ASN cc_start: 0.9036 (t0) cc_final: 0.8708 (t0) REVERT: M 150 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8013 (mtp85) REVERT: M 213 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6141 (mmt) REVERT: M 468 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7444 (mm-30) REVERT: M 470 LYS cc_start: 0.8610 (mptt) cc_final: 0.8279 (mmmt) REVERT: M 628 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: M 688 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: N 132 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8445 (ttpt) REVERT: O 215 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.8164 (mttp) REVERT: P 56 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8243 (mttp) REVERT: T 43 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8893 (tm-30) REVERT: X 123 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8037 (mt-10) REVERT: Z 49 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: c 43 LYS cc_start: 0.7911 (mtmp) cc_final: 0.7569 (mtmm) REVERT: c 143 MET cc_start: 0.8402 (mmm) cc_final: 0.8126 (mmm) REVERT: c 148 GLU cc_start: 0.8428 (tp30) cc_final: 0.8076 (tp30) REVERT: f 65 ASP cc_start: 0.8217 (m-30) cc_final: 0.7874 (m-30) REVERT: i 244 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8220 (ttp) REVERT: k 5 TYR cc_start: 0.9195 (m-10) cc_final: 0.8892 (m-10) REVERT: l 1 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.5456 (tmt) REVERT: l 176 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8185 (tpt90) REVERT: l 271 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7961 (mttt) REVERT: l 411 MET cc_start: 0.8018 (mmp) cc_final: 0.7731 (mmp) REVERT: m 46 ASN cc_start: 0.8808 (m-40) cc_final: 0.8525 (m110) REVERT: o 42 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6957 (ttp80) REVERT: p 66 GLN cc_start: 0.7566 (mp10) cc_final: 0.7298 (mp10) REVERT: r 103 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8943 (tt0) REVERT: r 243 MET cc_start: 0.8502 (mmm) cc_final: 0.7991 (tpp) REVERT: s 227 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7708 (tp30) REVERT: u 155 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7453 (pp20) REVERT: v 39 MET cc_start: 0.8069 (tpt) cc_final: 0.7863 (tpp) REVERT: v 70 LYS cc_start: 0.8729 (mtpm) cc_final: 0.8402 (mtpt) REVERT: w 95 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: w 267 GLU cc_start: 0.6929 (tp30) cc_final: 0.6666 (tp30) outliers start: 178 outliers final: 84 residues processed: 1218 average time/residue: 1.5883 time to fit residues: 2493.8029 Evaluate side-chains 1216 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1106 time to evaluate : 6.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 324 MET Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 712 LYS Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 36 ILE Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 42 ARG Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 311 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 261 optimal weight: 5.9990 chunk 700 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 456 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 778 optimal weight: 3.9990 chunk 646 optimal weight: 7.9990 chunk 360 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 257 optimal weight: 0.7980 chunk 408 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 116 ASN P 63 GLN U 11 ASN Z 33 GLN c 164 ASN f 61 GLN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS k 50 ASN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN l 479 ASN l 534 HIS ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 51 ASN r 139 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 69931 Z= 0.309 Angle : 0.595 11.131 94519 Z= 0.301 Chirality : 0.044 0.202 10191 Planarity : 0.005 0.062 11777 Dihedral : 13.790 177.098 10867 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.74 % Allowed : 13.65 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.58 (0.09), residues: 8172 helix: 1.28 (0.08), residues: 4290 sheet: -0.12 (0.25), residues: 410 loop : -0.65 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.010 0.001 HIS S 27 PHE 0.028 0.002 PHE i 292 TYR 0.020 0.002 TYR r 406 ARG 0.008 0.000 ARG g 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1120 time to evaluate : 6.320 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 THR cc_start: 0.8490 (t) cc_final: 0.8271 (t) REVERT: A 387 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: B 68 ARG cc_start: 0.8511 (mtp180) cc_final: 0.8302 (mtt180) REVERT: B 149 MET cc_start: 0.9126 (mmm) cc_final: 0.8902 (mmm) REVERT: C 52 ASP cc_start: 0.8494 (m-30) cc_final: 0.8286 (m-30) REVERT: C 154 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8084 (p0) REVERT: C 192 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9087 (mt) REVERT: E 23 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7581 (mtt-85) REVERT: F 57 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: F 95 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7437 (mt) REVERT: J 234 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: J 341 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: K 90 ASN cc_start: 0.9049 (t0) cc_final: 0.8726 (t0) REVERT: M 150 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8023 (mtp85) REVERT: M 213 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.6011 (mmt) REVERT: M 468 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: M 470 LYS cc_start: 0.8670 (mptt) cc_final: 0.8397 (mmmt) REVERT: M 628 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: M 688 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: O 215 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8190 (mttp) REVERT: P 56 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8262 (mttp) REVERT: Q 57 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: Q 308 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.6317 (p90) REVERT: T 43 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8876 (tm-30) REVERT: X 123 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8019 (mt-10) REVERT: X 129 GLU cc_start: 0.8414 (tt0) cc_final: 0.8200 (tt0) REVERT: Z 49 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: c 43 LYS cc_start: 0.7937 (mtmp) cc_final: 0.7578 (mtmm) REVERT: c 143 MET cc_start: 0.8419 (mmm) cc_final: 0.8135 (mmm) REVERT: d 134 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: e 111 ASP cc_start: 0.7087 (t0) cc_final: 0.6875 (t0) REVERT: f 61 GLN cc_start: 0.8438 (tp-100) cc_final: 0.7987 (tp40) REVERT: h 70 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: j 44 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7325 (tpp) REVERT: k 5 TYR cc_start: 0.9217 (m-10) cc_final: 0.8922 (m-10) REVERT: l 1 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5468 (tmt) REVERT: l 176 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8235 (tpt90) REVERT: l 271 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7966 (mttt) REVERT: l 411 MET cc_start: 0.8006 (mmp) cc_final: 0.7771 (mmp) REVERT: m 135 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8131 (t80) REVERT: o 106 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8163 (tmtt) REVERT: r 103 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8916 (tt0) REVERT: r 243 MET cc_start: 0.8539 (mmm) cc_final: 0.8026 (tpp) REVERT: s 227 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: u 155 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: v 39 MET cc_start: 0.8122 (tpt) cc_final: 0.7870 (tpp) REVERT: v 70 LYS cc_start: 0.8728 (mtpm) cc_final: 0.8388 (mtpt) REVERT: w 95 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: w 267 GLU cc_start: 0.6972 (tp30) cc_final: 0.6760 (tp30) outliers start: 196 outliers final: 110 residues processed: 1224 average time/residue: 1.6608 time to fit residues: 2663.4472 Evaluate side-chains 1233 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1092 time to evaluate : 6.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 213 MET Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 70 GLN Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 562 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 106 LYS Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain s residue 311 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain u residue 162 LYS Chi-restraints excluded: chain u residue 172 MET Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 750 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 443 optimal weight: 6.9990 chunk 568 optimal weight: 2.9990 chunk 440 optimal weight: 0.7980 chunk 655 optimal weight: 9.9990 chunk 434 optimal weight: 5.9990 chunk 775 optimal weight: 2.9990 chunk 485 optimal weight: 3.9990 chunk 473 optimal weight: 7.9990 chunk 358 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN L 88 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN N 116 ASN P 63 GLN U 11 ASN W 61 GLN Z 33 GLN c 164 ASN ** i 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 319 HIS j 26 GLN k 50 ASN l 34 ASN l 351 ASN l 479 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 51 ASN r 139 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 69931 Z= 0.341 Angle : 0.611 11.180 94519 Z= 0.309 Chirality : 0.045 0.202 10191 Planarity : 0.005 0.064 11777 Dihedral : 13.686 178.543 10867 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.99 % Rotamer: Outliers : 3.04 % Allowed : 13.77 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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 (0.09), residues: 8172 helix: 1.20 (0.08), residues: 4289 sheet: -0.16 (0.25), residues: 410 loop : -0.68 (0.10), residues: 3473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.010 0.001 HIS S 27 PHE 0.028 0.002 PHE i 292 TYR 0.022 0.002 TYR J 180 ARG 0.008 0.001 ARG g 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1107 time to evaluate : 6.383 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: C 52 ASP cc_start: 0.8498 (m-30) cc_final: 0.8270 (m-30) REVERT: C 154 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8092 (p0) REVERT: C 192 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9091 (mt) REVERT: E 23 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7598 (mtt-85) REVERT: F 40 ARG cc_start: 0.7106 (ptp-170) cc_final: 0.6601 (mpt-90) REVERT: F 95 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7458 (mt) REVERT: G 106 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6788 (mtmm) REVERT: J 234 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: J 341 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: K 90 ASN cc_start: 0.9049 (t0) cc_final: 0.8737 (t0) REVERT: M 150 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8129 (mtp85) REVERT: M 468 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7430 (mm-30) REVERT: M 470 LYS cc_start: 0.8678 (mptt) cc_final: 0.8412 (mmmt) REVERT: M 628 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: M 688 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: N 12 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7277 (mm-40) REVERT: O 215 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8177 (mttp) REVERT: P 56 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8314 (mttp) REVERT: Q 57 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: Q 236 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8907 (mt) REVERT: Q 308 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.6481 (p90) REVERT: T 43 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8895 (tm-30) REVERT: X 123 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8027 (mt-10) REVERT: X 129 GLU cc_start: 0.8523 (tt0) cc_final: 0.8303 (tt0) REVERT: Z 49 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7389 (mm-30) REVERT: c 43 LYS cc_start: 0.7965 (mtmp) cc_final: 0.7629 (mtmm) REVERT: c 143 MET cc_start: 0.8429 (mmm) cc_final: 0.8126 (mmm) REVERT: d 134 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6838 (mp10) REVERT: e 127 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8472 (ttpt) REVERT: f 61 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8035 (tp40) REVERT: f 65 ASP cc_start: 0.8321 (m-30) cc_final: 0.7977 (m-30) REVERT: h 70 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: i 18 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7276 (tpt) REVERT: k 5 TYR cc_start: 0.9220 (m-10) cc_final: 0.8940 (m-10) REVERT: l 1 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5897 (tmt) REVERT: l 176 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8259 (tpt90) REVERT: l 271 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7991 (mttt) REVERT: l 411 MET cc_start: 0.7993 (mmp) cc_final: 0.7788 (mmp) REVERT: m 135 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (t80) REVERT: o 106 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8165 (tmtt) REVERT: r 103 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8911 (tt0) REVERT: r 168 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: r 229 MET cc_start: 0.9121 (mtp) cc_final: 0.8818 (mtm) REVERT: r 243 MET cc_start: 0.8553 (mmm) cc_final: 0.8129 (tpp) REVERT: s 227 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7721 (tp30) REVERT: u 155 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: v 39 MET cc_start: 0.8159 (tpt) cc_final: 0.7928 (tpp) REVERT: v 70 LYS cc_start: 0.8734 (mtpm) cc_final: 0.8392 (mtpt) REVERT: w 95 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8106 (m-30) outliers start: 218 outliers final: 123 residues processed: 1222 average time/residue: 1.6455 time to fit residues: 2575.2487 Evaluate side-chains 1245 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1088 time to evaluate : 6.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain J residue 374 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 426 ASP Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 443 ASP Chi-restraints excluded: chain M residue 468 GLU Chi-restraints excluded: chain M residue 490 LEU Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 628 GLU Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 680 LEU Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain N residue 12 GLN Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 453 THR Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain V residue 124 LEU Chi-restraints excluded: chain V residue 141 VAL Chi-restraints excluded: chain W residue 49 SER Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain a residue 130 GLU Chi-restraints excluded: chain a residue 173 THR Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 188 ASP Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 120 SER Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 134 GLN Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 127 LYS Chi-restraints excluded: chain f residue 67 LEU Chi-restraints excluded: chain f residue 70 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 69 SER Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain h residue 70 GLN Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain h residue 80 LYS Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 100 MET Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 321 LYS Chi-restraints excluded: chain i residue 323 MET Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain k residue 61 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 71 LEU Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 111 ASP Chi-restraints excluded: chain l residue 133 THR Chi-restraints excluded: chain l residue 151 SER Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 271 LYS Chi-restraints excluded: chain l residue 393 ASP Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 484 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain l residue 581 LYS Chi-restraints excluded: chain l residue 600 THR Chi-restraints excluded: chain m residue 135 PHE Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 106 LYS Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 14 GLN Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 110 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 47 GLU Chi-restraints excluded: chain r residue 103 GLN Chi-restraints excluded: chain r residue 140 THR Chi-restraints excluded: chain r residue 168 GLN Chi-restraints excluded: chain r residue 179 ILE Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 177 THR Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain s residue 311 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain u residue 162 LYS Chi-restraints excluded: chain u residue 172 MET Chi-restraints excluded: chain v residue 21 ARG Chi-restraints excluded: chain v residue 22 MET Chi-restraints excluded: chain v residue 38 GLU Chi-restraints excluded: chain w residue 95 ASP Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 480 optimal weight: 0.8980 chunk 309 optimal weight: 0.7980 chunk 463 optimal weight: 6.9990 chunk 233 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 493 optimal weight: 0.9980 chunk 528 optimal weight: 0.0970 chunk 383 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 609 optimal weight: 6.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 GLN F 31 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 52 ASN N 116 ASN N 135 GLN P 63 GLN T 43 GLN U 11 ASN Z 33 GLN c 164 ASN i 47 ASN i 171 ASN i 319 HIS j 26 GLN k 50 ASN ** l 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN l 479 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 51 ASN r 139 GLN ** u 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 GLN v 110 GLN w 107 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 69931 Z= 0.139 Angle : 0.516 10.542 94519 Z= 0.260 Chirality : 0.040 0.179 10191 Planarity : 0.004 0.062 11777 Dihedral : 12.964 179.237 10867 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 1.63 % Allowed : 15.35 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.92 (0.09), residues: 8172 helix: 1.59 (0.08), residues: 4278 sheet: 0.09 (0.24), residues: 428 loop : -0.54 (0.10), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP u 86 HIS 0.005 0.001 HIS J 37 PHE 0.032 0.001 PHE i 292 TYR 0.021 0.001 TYR r 256 ARG 0.008 0.000 ARG g 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1160 time to evaluate : 6.234 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: A 387 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: B 149 MET cc_start: 0.9110 (mmm) cc_final: 0.8847 (mmm) REVERT: C 52 ASP cc_start: 0.8426 (m-30) cc_final: 0.8159 (m-30) REVERT: C 154 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7938 (p0) REVERT: C 192 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9012 (mt) REVERT: E 110 THR cc_start: 0.8372 (p) cc_final: 0.8144 (m) REVERT: F 40 ARG cc_start: 0.7086 (ptp-170) cc_final: 0.6602 (mpt-90) REVERT: F 95 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7485 (mt) REVERT: J 296 PHE cc_start: 0.8289 (p90) cc_final: 0.8060 (p90) REVERT: J 341 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6940 (mp10) REVERT: K 90 ASN cc_start: 0.8996 (t0) cc_final: 0.8683 (t0) REVERT: M 150 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7897 (mtp85) REVERT: M 434 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8205 (m) REVERT: M 470 LYS cc_start: 0.8591 (mptt) cc_final: 0.8324 (mmmt) REVERT: M 688 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: O 215 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8190 (mttp) REVERT: Q 308 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6444 (p90) REVERT: T 43 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8854 (tm-30) REVERT: c 43 LYS cc_start: 0.7914 (mtmp) cc_final: 0.7569 (mtmm) REVERT: c 143 MET cc_start: 0.8403 (mmm) cc_final: 0.8125 (mmm) REVERT: f 61 GLN cc_start: 0.8504 (tp-100) cc_final: 0.8024 (tp40) REVERT: i 18 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7216 (tpt) REVERT: i 244 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8167 (ttp) REVERT: j 44 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7234 (tpp) REVERT: j 69 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7780 (mp) REVERT: k 5 TYR cc_start: 0.9157 (m-10) cc_final: 0.8908 (m-10) REVERT: l 176 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (tpt90) REVERT: m 46 ASN cc_start: 0.8824 (m-40) cc_final: 0.8557 (m110) REVERT: r 229 MET cc_start: 0.9086 (mtp) cc_final: 0.8797 (mtm) REVERT: r 243 MET cc_start: 0.8419 (mmm) cc_final: 0.7811 (tpp) REVERT: s 156 MET cc_start: 0.8027 (mmp) cc_final: 0.7696 (mmp) REVERT: s 227 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: u 155 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7347 (pp20) REVERT: v 70 LYS cc_start: 0.8717 (mtpm) cc_final: 0.8385 (mtpt) REVERT: w 291 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8730 (m-10) outliers start: 117 outliers final: 45 residues processed: 1215 average time/residue: 1.5880 time to fit residues: 2492.9884 Evaluate side-chains 1156 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1092 time to evaluate : 6.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 65 ASP Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain o residue 114 LYS Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain u residue 155 GLU Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 805 random chunks: chunk 705 optimal weight: 0.0030 chunk 743 optimal weight: 5.9990 chunk 678 optimal weight: 3.9990 chunk 723 optimal weight: 0.8980 chunk 435 optimal weight: 9.9990 chunk 314 optimal weight: 2.9990 chunk 567 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 653 optimal weight: 4.9990 chunk 683 optimal weight: 0.9980 chunk 720 optimal weight: 1.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN F 25 GLN ** I 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 514 ASN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 52 ASN N 116 ASN N 135 GLN P 63 GLN T 43 GLN U 11 ASN Z 33 GLN c 127 ASN c 164 ASN i 47 ASN i 171 ASN i 319 HIS k 50 ASN l 170 GLN ** l 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 351 ASN l 479 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 141 GLN r 51 ASN r 139 GLN u 77 HIS v 54 GLN w 107 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 69931 Z= 0.186 Angle : 0.542 12.079 94519 Z= 0.271 Chirality : 0.041 0.183 10191 Planarity : 0.004 0.058 11777 Dihedral : 12.723 178.565 10863 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 1.52 % Allowed : 16.08 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.19 % 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: 0.95 (0.09), residues: 8172 helix: 1.60 (0.08), residues: 4294 sheet: 0.05 (0.24), residues: 439 loop : -0.50 (0.11), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP u 86 HIS 0.006 0.001 HIS J 37 PHE 0.030 0.001 PHE i 292 TYR 0.018 0.001 TYR l 422 ARG 0.008 0.000 ARG g 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16344 Ramachandran restraints generated. 8172 Oldfield, 0 Emsley, 8172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1208 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1099 time to evaluate : 6.250 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: A 359 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7975 (mtm-85) REVERT: A 387 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: C 52 ASP cc_start: 0.8382 (m-30) cc_final: 0.8108 (m-30) REVERT: C 154 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8016 (p0) REVERT: C 192 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9014 (mt) REVERT: E 110 THR cc_start: 0.8393 (p) cc_final: 0.8142 (m) REVERT: F 40 ARG cc_start: 0.7091 (ptp-170) cc_final: 0.6604 (mpt-90) REVERT: F 46 LYS cc_start: 0.8254 (mtmp) cc_final: 0.8051 (mtmm) REVERT: F 95 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7420 (mt) REVERT: J 341 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: K 90 ASN cc_start: 0.9009 (t0) cc_final: 0.8694 (t0) REVERT: M 150 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8016 (mtp85) REVERT: M 470 LYS cc_start: 0.8583 (mptt) cc_final: 0.8298 (mmmt) REVERT: M 688 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: P 56 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8326 (mttp) REVERT: Q 308 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.6253 (p90) REVERT: Z 49 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: c 43 LYS cc_start: 0.7926 (mtmp) cc_final: 0.7584 (mtmm) REVERT: c 143 MET cc_start: 0.8399 (mmm) cc_final: 0.8129 (mmm) REVERT: f 61 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8141 (tp40) REVERT: i 18 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7250 (tpt) REVERT: j 44 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7254 (tpp) REVERT: j 69 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7864 (mp) REVERT: k 5 TYR cc_start: 0.9156 (m-10) cc_final: 0.8894 (m-10) REVERT: l 1 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6745 (pp-130) REVERT: l 176 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8204 (tpt90) REVERT: l 410 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8402 (tt) REVERT: l 411 MET cc_start: 0.8104 (mmp) cc_final: 0.7841 (mmp) REVERT: r 229 MET cc_start: 0.9122 (mtp) cc_final: 0.8827 (mtm) REVERT: r 243 MET cc_start: 0.8419 (mmm) cc_final: 0.7859 (tpp) REVERT: s 156 MET cc_start: 0.8090 (mmp) cc_final: 0.7764 (mmp) REVERT: s 227 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: u 6 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: v 70 LYS cc_start: 0.8750 (mtpm) cc_final: 0.8402 (mtpt) REVERT: w 291 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8722 (m-10) outliers start: 109 outliers final: 55 residues processed: 1160 average time/residue: 1.6078 time to fit residues: 2405.5095 Evaluate side-chains 1156 residues out of total 7204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1081 time to evaluate : 6.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 341 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain M residue 150 ARG Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 361 VAL Chi-restraints excluded: chain M residue 434 SER Chi-restraints excluded: chain M residue 559 ASP Chi-restraints excluded: chain M residue 636 TYR Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 166 ASP Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 56 LYS Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain T residue 32 SER Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain V residue 115 CYS Chi-restraints excluded: chain X residue 101 ASN Chi-restraints excluded: chain Y residue 77 SER Chi-restraints excluded: chain Z residue 49 GLU Chi-restraints excluded: chain b residue 17 GLU Chi-restraints excluded: chain c residue 165 ASP Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain i residue 18 MET Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain i residue 87 THR Chi-restraints excluded: chain i residue 149 ILE Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain i residue 244 MET Chi-restraints excluded: chain i residue 320 THR Chi-restraints excluded: chain i residue 336 VAL Chi-restraints excluded: chain j residue 31 SER Chi-restraints excluded: chain j residue 44 MET Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 ASN Chi-restraints excluded: chain j residue 86 THR Chi-restraints excluded: chain k residue 24 SER Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 21 MET Chi-restraints excluded: chain l residue 176 ARG Chi-restraints excluded: chain l residue 410 LEU Chi-restraints excluded: chain l residue 500 LEU Chi-restraints excluded: chain l residue 504 LEU Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain p residue 114 MET Chi-restraints excluded: chain p residue 144 THR Chi-restraints excluded: chain r residue 247 THR Chi-restraints excluded: chain r residue 255 ASN Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 227 GLU Chi-restraints excluded: chain s residue 258 ASN Chi-restraints excluded: chain s residue 296 LEU Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 6 GLU Chi-restraints excluded: chain u residue 131 VAL Chi-restraints excluded: chain u residue 132 LYS Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 241 TYR Chi-restraints excluded: chain w residue 262 GLU Chi-restraints excluded: chain w residue 287 ASP Chi-restraints excluded: chain w residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/iotbx/cli_parser.py", line 939, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.7344 > 50: distance: 83 - 88: 33.858 distance: 88 - 89: 41.884 distance: 89 - 90: 29.847 distance: 89 - 92: 24.984 distance: 90 - 91: 3.950 distance: 90 - 98: 12.048 distance: 92 - 93: 13.001 distance: 93 - 94: 11.179 distance: 93 - 95: 12.933 distance: 94 - 96: 11.853 distance: 96 - 97: 12.753 distance: 98 - 99: 11.991 distance: 99 - 100: 10.465 distance: 99 - 102: 15.747 distance: 100 - 101: 9.990 distance: 100 - 105: 4.231 distance: 102 - 103: 17.683 distance: 102 - 104: 16.081 distance: 105 - 106: 6.179 distance: 105 - 111: 10.434 distance: 106 - 107: 16.106 distance: 106 - 109: 8.373 distance: 107 - 108: 12.361 distance: 107 - 112: 5.372 distance: 108 - 141: 11.639 distance: 109 - 110: 12.774 distance: 110 - 111: 12.218 distance: 112 - 113: 8.102 distance: 113 - 116: 6.075 distance: 114 - 115: 11.003 distance: 114 - 121: 8.272 distance: 115 - 148: 15.553 distance: 116 - 117: 5.854 distance: 117 - 118: 11.376 distance: 118 - 119: 11.490 distance: 118 - 120: 26.718 distance: 121 - 122: 8.682 distance: 122 - 123: 12.050 distance: 122 - 125: 8.251 distance: 123 - 124: 12.466 distance: 123 - 129: 6.683 distance: 124 - 156: 14.597 distance: 125 - 126: 14.665 distance: 126 - 127: 16.448 distance: 126 - 128: 9.492 distance: 130 - 131: 8.694 distance: 130 - 133: 8.519 distance: 131 - 132: 20.568 distance: 131 - 141: 7.080 distance: 132 - 164: 33.842 distance: 133 - 134: 7.039 distance: 134 - 135: 6.631 distance: 134 - 136: 3.335 distance: 135 - 137: 9.330 distance: 136 - 138: 9.095 distance: 137 - 139: 4.896 distance: 138 - 139: 7.145 distance: 139 - 140: 17.286 distance: 141 - 142: 3.278 distance: 142 - 143: 5.901 distance: 142 - 145: 3.768 distance: 143 - 144: 18.736 distance: 143 - 148: 20.505 distance: 144 - 175: 12.756 distance: 145 - 146: 6.379 distance: 145 - 147: 8.448 distance: 148 - 149: 12.780 distance: 149 - 150: 7.750 distance: 149 - 152: 21.088 distance: 150 - 151: 9.953 distance: 150 - 156: 9.256 distance: 151 - 182: 12.050 distance: 152 - 153: 15.758 distance: 152 - 154: 15.974 distance: 153 - 155: 16.939 distance: 156 - 157: 5.797 distance: 157 - 158: 10.944 distance: 157 - 160: 11.725 distance: 158 - 159: 8.257 distance: 158 - 164: 13.027 distance: 159 - 189: 12.963 distance: 160 - 161: 6.175 distance: 161 - 162: 19.672 distance: 161 - 163: 7.712 distance: 164 - 165: 12.023 distance: 165 - 166: 30.478 distance: 165 - 168: 16.941 distance: 166 - 175: 18.995 distance: 167 - 198: 17.040 distance: 168 - 169: 14.525 distance: 169 - 170: 23.899 distance: 169 - 171: 23.792 distance: 170 - 172: 19.547 distance: 171 - 173: 19.120 distance: 172 - 174: 26.216 distance: 173 - 174: 15.307