Starting phenix.real_space_refine on Thu Feb 22 20:27:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/02_2024/6co7_7542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/02_2024/6co7_7542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/02_2024/6co7_7542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/02_2024/6co7_7542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/02_2024/6co7_7542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6co7_7542/02_2024/6co7_7542_updated.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 20 5.49 5 S 188 5.16 5 Na 3 4.78 5 C 23024 2.51 5 N 5648 2.21 5 O 6368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 130": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A ARG 935": "NH1" <-> "NH2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A ARG 947": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 642": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 820": "NH1" <-> "NH2" Residue "B ARG 895": "NH1" <-> "NH2" Residue "B ARG 935": "NH1" <-> "NH2" Residue "B ARG 941": "NH1" <-> "NH2" Residue "B ARG 947": "NH1" <-> "NH2" Residue "B ARG 960": "NH1" <-> "NH2" Residue "B ARG 1016": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "B ARG 1132": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 160": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 642": "NH1" <-> "NH2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C ARG 714": "NH1" <-> "NH2" Residue "C ARG 820": "NH1" <-> "NH2" Residue "C ARG 895": "NH1" <-> "NH2" Residue "C ARG 935": "NH1" <-> "NH2" Residue "C ARG 941": "NH1" <-> "NH2" Residue "C ARG 947": "NH1" <-> "NH2" Residue "C ARG 960": "NH1" <-> "NH2" Residue "C ARG 1016": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C ARG 1132": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 642": "NH1" <-> "NH2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D ARG 714": "NH1" <-> "NH2" Residue "D ARG 820": "NH1" <-> "NH2" Residue "D ARG 895": "NH1" <-> "NH2" Residue "D ARG 935": "NH1" <-> "NH2" Residue "D ARG 941": "NH1" <-> "NH2" Residue "D ARG 947": "NH1" <-> "NH2" Residue "D ARG 960": "NH1" <-> "NH2" Residue "D ARG 1016": "NH1" <-> "NH2" Residue "D ARG 1091": "NH1" <-> "NH2" Residue "D ARG 1132": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35255 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "C" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 8422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8422 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 41, 'TRANS': 1019} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 366 Unusual residues: {' CA': 1, ' NA': 3, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 363 Unusual residues: {' CA': 1, 'CLR': 1, 'POV': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 486 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 10, 'POV:plan-2': 8, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 79 Time building chain proxies: 19.02, per 1000 atoms: 0.54 Number of scatterers: 35255 At special positions: 0 Unit cell: (149.35, 149.35, 159.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 188 16.00 P 20 15.00 Na 3 11.00 O 6368 8.00 N 5648 7.00 C 23024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A1017 " " NAG F 1 " - " ASN B1017 " " NAG G 1 " - " ASN C1017 " " NAG H 1 " - " ASN D1017 " Time building additional restraints: 13.49 Conformation dependent library (CDL) restraints added in 6.1 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 180 helices and 12 sheets defined 57.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.81 Creating SS restraints... Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 153 through 170 removed outlier: 4.082A pdb=" N ILE A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 375 through 385 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 434 through 440 Processing helix chain 'A' and resid 450 through 462 removed outlier: 5.294A pdb=" N ALA A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA A 456 " --> pdb=" O THR A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.708A pdb=" N LEU A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'A' and resid 593 through 601 Processing helix chain 'A' and resid 606 through 626 Processing helix chain 'A' and resid 634 through 658 Processing helix chain 'A' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 685 Processing helix chain 'A' and resid 689 through 692 No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 695 through 705 Processing helix chain 'A' and resid 715 through 723 removed outlier: 3.975A pdb=" N TYR A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 828 through 835 removed outlier: 3.841A pdb=" N PHE A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 860 Processing helix chain 'A' and resid 871 through 873 No H-bonds generated for 'chain 'A' and resid 871 through 873' Processing helix chain 'A' and resid 877 through 898 Processing helix chain 'A' and resid 905 through 912 Processing helix chain 'A' and resid 917 through 937 removed outlier: 4.279A pdb=" N PHE A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE A 937 " --> pdb=" O ILE A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 961 " --> pdb=" O PHE A 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 962 " --> pdb=" O ILE A 958 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 967 " --> pdb=" O GLN A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1007 Proline residue: A 973 - end of helix removed outlier: 3.760A pdb=" N GLN A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A 983 " --> pdb=" O GLN A 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL A1027 " --> pdb=" O ILE A1023 " (cutoff:3.500A) Proline residue: A1030 - end of helix removed outlier: 3.565A pdb=" N MET A1034 " --> pdb=" O PRO A1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR A1035 " --> pdb=" O TYR A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1043 No H-bonds generated for 'chain 'A' and resid 1040 through 1043' Processing helix chain 'A' and resid 1058 through 1074 Proline residue: A1063 - end of helix Processing helix chain 'A' and resid 1077 through 1113 removed outlier: 4.232A pdb=" N GLU A1090 " --> pdb=" O ASN A1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG A1091 " --> pdb=" O TYR A1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A1097 " --> pdb=" O GLN A1093 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS A1098 " --> pdb=" O GLU A1094 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR A1105 " --> pdb=" O LYS A1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1135 removed outlier: 3.823A pdb=" N LEU A1128 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A1129 " --> pdb=" O GLY A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1181 Processing helix chain 'A' and resid 1184 through 1209 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 153 through 170 removed outlier: 4.081A pdb=" N ILE B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 375 through 385 Processing helix chain 'B' and resid 405 through 416 Processing helix chain 'B' and resid 421 through 431 Processing helix chain 'B' and resid 434 through 440 Processing helix chain 'B' and resid 450 through 462 removed outlier: 5.294A pdb=" N ALA B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.709A pdb=" N LEU B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 528 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 579 through 589 Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 606 through 626 Processing helix chain 'B' and resid 634 through 658 Processing helix chain 'B' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 689 through 692 No H-bonds generated for 'chain 'B' and resid 689 through 692' Processing helix chain 'B' and resid 695 through 705 Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.974A pdb=" N TYR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 828 through 835 removed outlier: 3.841A pdb=" N PHE B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 860 Processing helix chain 'B' and resid 871 through 873 No H-bonds generated for 'chain 'B' and resid 871 through 873' Processing helix chain 'B' and resid 877 through 898 Processing helix chain 'B' and resid 905 through 912 Processing helix chain 'B' and resid 917 through 937 removed outlier: 4.279A pdb=" N PHE B 936 " --> pdb=" O ILE B 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE B 955 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER B 961 " --> pdb=" O PHE B 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU B 962 " --> pdb=" O ILE B 958 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE B 964 " --> pdb=" O ARG B 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 967 " --> pdb=" O GLN B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 1007 Proline residue: B 973 - end of helix removed outlier: 3.760A pdb=" N GLN B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN B 983 " --> pdb=" O GLN B 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP B 984 " --> pdb=" O LYS B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix removed outlier: 3.566A pdb=" N MET B1034 " --> pdb=" O PRO B1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR B1035 " --> pdb=" O TYR B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1043 No H-bonds generated for 'chain 'B' and resid 1040 through 1043' Processing helix chain 'B' and resid 1058 through 1074 Proline residue: B1063 - end of helix Processing helix chain 'B' and resid 1077 through 1113 removed outlier: 4.233A pdb=" N GLU B1090 " --> pdb=" O ASN B1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG B1091 " --> pdb=" O TYR B1087 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP B1095 " --> pdb=" O ARG B1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B1097 " --> pdb=" O GLN B1093 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS B1098 " --> pdb=" O GLU B1094 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR B1105 " --> pdb=" O LYS B1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP B1106 " --> pdb=" O PHE B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1135 removed outlier: 3.823A pdb=" N LEU B1128 " --> pdb=" O LEU B1124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B1129 " --> pdb=" O GLY B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1181 Processing helix chain 'B' and resid 1184 through 1209 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 153 through 170 removed outlier: 4.081A pdb=" N ILE C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 221 No H-bonds generated for 'chain 'C' and resid 218 through 221' Processing helix chain 'C' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 329 through 338 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 375 through 385 Processing helix chain 'C' and resid 405 through 416 Processing helix chain 'C' and resid 421 through 431 Processing helix chain 'C' and resid 434 through 440 Processing helix chain 'C' and resid 450 through 462 removed outlier: 5.293A pdb=" N ALA C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA C 456 " --> pdb=" O THR C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 485 through 493 Processing helix chain 'C' and resid 500 through 510 removed outlier: 3.708A pdb=" N LEU C 504 " --> pdb=" O THR C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 542 through 544 No H-bonds generated for 'chain 'C' and resid 542 through 544' Processing helix chain 'C' and resid 579 through 589 Processing helix chain 'C' and resid 593 through 601 Processing helix chain 'C' and resid 606 through 626 Processing helix chain 'C' and resid 634 through 658 Processing helix chain 'C' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 685 Processing helix chain 'C' and resid 689 through 692 No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 695 through 705 Processing helix chain 'C' and resid 715 through 723 removed outlier: 3.975A pdb=" N TYR C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 819 Processing helix chain 'C' and resid 828 through 835 removed outlier: 3.842A pdb=" N PHE C 833 " --> pdb=" O ARG C 829 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 860 Processing helix chain 'C' and resid 871 through 873 No H-bonds generated for 'chain 'C' and resid 871 through 873' Processing helix chain 'C' and resid 877 through 898 Processing helix chain 'C' and resid 905 through 912 Processing helix chain 'C' and resid 917 through 937 removed outlier: 4.280A pdb=" N PHE C 936 " --> pdb=" O ILE C 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE C 937 " --> pdb=" O ILE C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C 961 " --> pdb=" O PHE C 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU C 962 " --> pdb=" O ILE C 958 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE C 964 " --> pdb=" O ARG C 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 967 " --> pdb=" O GLN C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1007 Proline residue: C 973 - end of helix removed outlier: 3.759A pdb=" N GLN C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 983 " --> pdb=" O GLN C 979 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP C 984 " --> pdb=" O LYS C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL C1027 " --> pdb=" O ILE C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix removed outlier: 3.565A pdb=" N MET C1034 " --> pdb=" O PRO C1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C1035 " --> pdb=" O TYR C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1043 No H-bonds generated for 'chain 'C' and resid 1040 through 1043' Processing helix chain 'C' and resid 1058 through 1074 Proline residue: C1063 - end of helix Processing helix chain 'C' and resid 1077 through 1113 removed outlier: 4.231A pdb=" N GLU C1090 " --> pdb=" O ASN C1086 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG C1091 " --> pdb=" O TYR C1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP C1095 " --> pdb=" O ARG C1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP C1097 " --> pdb=" O GLN C1093 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS C1098 " --> pdb=" O GLU C1094 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR C1105 " --> pdb=" O LYS C1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C1106 " --> pdb=" O PHE C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1135 removed outlier: 3.823A pdb=" N LEU C1128 " --> pdb=" O LEU C1124 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C1129 " --> pdb=" O GLY C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1155 through 1181 Processing helix chain 'C' and resid 1184 through 1209 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 153 through 170 removed outlier: 4.082A pdb=" N ILE D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.193A pdb=" N MET D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 221 No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 268 through 279 removed outlier: 3.944A pdb=" N MET D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 315 Processing helix chain 'D' and resid 329 through 338 Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 375 through 385 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 421 through 431 Processing helix chain 'D' and resid 434 through 440 Processing helix chain 'D' and resid 450 through 462 removed outlier: 5.294A pdb=" N ALA D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA D 456 " --> pdb=" O THR D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 500 through 510 removed outlier: 3.708A pdb=" N LEU D 504 " --> pdb=" O THR D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 606 through 626 Processing helix chain 'D' and resid 634 through 658 Processing helix chain 'D' and resid 660 through 668 removed outlier: 3.705A pdb=" N GLN D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 685 Processing helix chain 'D' and resid 689 through 692 No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 695 through 705 Processing helix chain 'D' and resid 715 through 723 removed outlier: 3.974A pdb=" N TYR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 749 removed outlier: 3.595A pdb=" N GLU D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 819 Processing helix chain 'D' and resid 828 through 835 removed outlier: 3.842A pdb=" N PHE D 833 " --> pdb=" O ARG D 829 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 860 Processing helix chain 'D' and resid 871 through 873 No H-bonds generated for 'chain 'D' and resid 871 through 873' Processing helix chain 'D' and resid 877 through 898 Processing helix chain 'D' and resid 905 through 912 Processing helix chain 'D' and resid 917 through 937 removed outlier: 4.280A pdb=" N PHE D 936 " --> pdb=" O ILE D 932 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE D 937 " --> pdb=" O ILE D 933 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 967 removed outlier: 5.229A pdb=" N ILE D 955 " --> pdb=" O SER D 951 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE D 956 " --> pdb=" O LEU D 952 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER D 961 " --> pdb=" O PHE D 957 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU D 962 " --> pdb=" O ILE D 958 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN D 963 " --> pdb=" O VAL D 959 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE D 964 " --> pdb=" O ARG D 960 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL D 967 " --> pdb=" O GLN D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 1007 Proline residue: D 973 - end of helix removed outlier: 3.760A pdb=" N GLN D 979 " --> pdb=" O LEU D 975 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN D 983 " --> pdb=" O GLN D 979 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP D 984 " --> pdb=" O LYS D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1035 removed outlier: 3.778A pdb=" N VAL D1027 " --> pdb=" O ILE D1023 " (cutoff:3.500A) Proline residue: D1030 - end of helix removed outlier: 3.566A pdb=" N MET D1034 " --> pdb=" O PRO D1030 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR D1035 " --> pdb=" O TYR D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1043 No H-bonds generated for 'chain 'D' and resid 1040 through 1043' Processing helix chain 'D' and resid 1058 through 1074 Proline residue: D1063 - end of helix Processing helix chain 'D' and resid 1077 through 1113 removed outlier: 4.232A pdb=" N GLU D1090 " --> pdb=" O ASN D1086 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG D1091 " --> pdb=" O TYR D1087 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP D1095 " --> pdb=" O ARG D1091 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D1097 " --> pdb=" O GLN D1093 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS D1098 " --> pdb=" O GLU D1094 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR D1105 " --> pdb=" O LYS D1101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP D1106 " --> pdb=" O PHE D1102 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1135 removed outlier: 3.824A pdb=" N LEU D1128 " --> pdb=" O LEU D1124 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D1129 " --> pdb=" O GLY D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1155 through 1181 Processing helix chain 'D' and resid 1184 through 1209 Processing sheet with id= A, first strand: chain 'A' and resid 46 through 48 Processing sheet with id= B, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 111 through 115 removed outlier: 6.633A pdb=" N PHE A 253 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET A 114 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 255 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 46 through 48 Processing sheet with id= E, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= F, first strand: chain 'B' and resid 111 through 115 removed outlier: 6.634A pdb=" N PHE B 253 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET B 114 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU B 255 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 46 through 48 Processing sheet with id= H, first strand: chain 'C' and resid 97 through 99 Processing sheet with id= I, first strand: chain 'C' and resid 111 through 115 removed outlier: 6.633A pdb=" N PHE C 253 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET C 114 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 255 " --> pdb=" O MET C 114 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 46 through 48 Processing sheet with id= K, first strand: chain 'D' and resid 97 through 99 Processing sheet with id= L, first strand: chain 'D' and resid 111 through 115 removed outlier: 6.634A pdb=" N PHE D 253 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N MET D 114 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU D 255 " --> pdb=" O MET D 114 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4932 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: 11.53 Time building geometry restraints manager: 14.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5620 1.31 - 1.43: 8968 1.43 - 1.56: 20904 1.56 - 1.68: 88 1.68 - 1.81: 344 Bond restraints: 35924 Sorted by residual: bond pdb=" C MET C1007 " pdb=" N PHE C1008 " ideal model delta sigma weight residual 1.330 1.481 -0.151 1.21e-02 6.83e+03 1.56e+02 bond pdb=" C MET A1007 " pdb=" N PHE A1008 " ideal model delta sigma weight residual 1.330 1.481 -0.150 1.21e-02 6.83e+03 1.54e+02 bond pdb=" C MET D1007 " pdb=" N PHE D1008 " ideal model delta sigma weight residual 1.330 1.481 -0.150 1.21e-02 6.83e+03 1.54e+02 bond pdb=" C MET B1007 " pdb=" N PHE B1008 " ideal model delta sigma weight residual 1.330 1.480 -0.150 1.21e-02 6.83e+03 1.53e+02 bond pdb=" C29 POV B3004 " pdb="C210 POV B3004 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 35919 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.05: 976 107.05 - 113.87: 19883 113.87 - 120.68: 15101 120.68 - 127.50: 12024 127.50 - 134.32: 344 Bond angle restraints: 48328 Sorted by residual: angle pdb=" N PRO B 8 " pdb=" CA PRO B 8 " pdb=" CB PRO B 8 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.47e+01 angle pdb=" N PRO C 8 " pdb=" CA PRO C 8 " pdb=" CB PRO C 8 " ideal model delta sigma weight residual 103.36 110.44 -7.08 8.80e-01 1.29e+00 6.47e+01 angle pdb=" N PRO D 8 " pdb=" CA PRO D 8 " pdb=" CB PRO D 8 " ideal model delta sigma weight residual 103.36 110.42 -7.06 8.80e-01 1.29e+00 6.44e+01 angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" CB PRO A 8 " ideal model delta sigma weight residual 103.36 110.42 -7.06 8.80e-01 1.29e+00 6.43e+01 angle pdb=" N PRO D 50 " pdb=" CA PRO D 50 " pdb=" CB PRO D 50 " ideal model delta sigma weight residual 103.25 110.60 -7.35 1.05e+00 9.07e-01 4.90e+01 ... (remaining 48323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 21212 25.39 - 50.79: 696 50.79 - 76.18: 120 76.18 - 101.57: 32 101.57 - 126.96: 12 Dihedral angle restraints: 22072 sinusoidal: 9704 harmonic: 12368 Sorted by residual: dihedral pdb=" CA SER C1010 " pdb=" C SER C1010 " pdb=" N PRO C1011 " pdb=" CA PRO C1011 " ideal model delta harmonic sigma weight residual 180.00 152.76 27.24 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER A1010 " pdb=" C SER A1010 " pdb=" N PRO A1011 " pdb=" CA PRO A1011 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER D1010 " pdb=" C SER D1010 " pdb=" N PRO D1011 " pdb=" CA PRO D1011 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 22069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3634 0.058 - 0.115: 1339 0.115 - 0.173: 305 0.173 - 0.231: 88 0.231 - 0.289: 10 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.97e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.94e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.76e+00 ... (remaining 5373 not shown) Planarity restraints: 5996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A3011 " 0.147 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV A3011 " -0.351 2.00e-02 2.50e+03 pdb="C210 POV A3011 " 0.345 2.00e-02 2.50e+03 pdb="C211 POV A3011 " -0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C3011 " -0.146 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV C3011 " 0.351 2.00e-02 2.50e+03 pdb="C210 POV C3011 " -0.345 2.00e-02 2.50e+03 pdb="C211 POV C3011 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B3011 " 0.147 2.00e-02 2.50e+03 2.66e-01 7.08e+02 pdb=" C29 POV B3011 " -0.351 2.00e-02 2.50e+03 pdb="C210 POV B3011 " 0.345 2.00e-02 2.50e+03 pdb="C211 POV B3011 " -0.140 2.00e-02 2.50e+03 ... (remaining 5993 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 76 2.64 - 3.20: 29590 3.20 - 3.77: 51404 3.77 - 4.33: 72316 4.33 - 4.90: 119864 Nonbonded interactions: 273250 Sorted by model distance: nonbonded pdb="NA NA A4001 " pdb="NA NA A4002 " model vdw 2.070 1.900 nonbonded pdb=" O VAL B 859 " pdb=" OG SER C1010 " model vdw 2.384 2.440 nonbonded pdb=" O VAL A 859 " pdb=" OG SER B1010 " model vdw 2.384 2.440 nonbonded pdb=" O VAL C 859 " pdb=" OG SER D1010 " model vdw 2.390 2.440 nonbonded pdb=" OG SER A1010 " pdb=" O VAL D 859 " model vdw 2.393 2.440 ... (remaining 273245 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 'A' and (resid 6 through 1210 or (resid 3002 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3004 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3006 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3007 or resid 3009)) selection = (chain 'B' and (resid 6 through 1210 or (resid 3001 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3003 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3005 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3006 or (resid 3008 and (name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C310 or name C311 or name C312)))) selection = (chain 'C' and (resid 6 through 1210 or (resid 3001 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3003 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3005 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or resid 3006 or (resid 3008 and (name C31 or na \ me C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 o \ r name C39 or name C310 or name C311 or name C312)))) selection = (chain 'D' and (resid 6 through 1210 or (resid 3012 and (name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C310 or name C311 or name C312 or name C313 or name C314 or name C315) \ ) or (resid 3014 and (name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C210 or name C211 or name C212 or name C213)) or (resid 3001 \ and (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or nam \ e C37 or name C38 or name C39)) or (resid 3002 and (name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C310 or name C311 or name C312 or name C313 or name C314 or name C315 or na \ me C316)) or (resid 3004 and (name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37 or name C38 or name C39 or name C310 or name C311 \ or name C312)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.020 Extract box with map and model: 14.320 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 90.110 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.250 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.202 35924 Z= 0.686 Angle : 1.390 20.322 48328 Z= 0.794 Chirality : 0.064 0.289 5376 Planarity : 0.012 0.266 5992 Dihedral : 14.009 126.964 14072 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 0.33 % Allowed : 2.44 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.11), residues: 4196 helix: -0.51 (0.09), residues: 2544 sheet: -1.65 (0.31), residues: 180 loop : -2.67 (0.14), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 885 HIS 0.004 0.001 HIS D1126 PHE 0.015 0.002 PHE D1085 TYR 0.012 0.001 TYR B 229 ARG 0.009 0.001 ARG B1059 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 784 time to evaluate : 3.708 Fit side-chains REVERT: A 107 LYS cc_start: 0.6801 (mttm) cc_final: 0.6510 (pttp) REVERT: A 112 LEU cc_start: 0.6264 (tt) cc_final: 0.6026 (tt) REVERT: A 158 MET cc_start: 0.6500 (ttm) cc_final: 0.6268 (tpp) REVERT: A 184 MET cc_start: 0.5139 (mpp) cc_final: 0.4869 (mtm) REVERT: A 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6990 (t0) REVERT: A 260 THR cc_start: 0.7684 (p) cc_final: 0.7472 (p) REVERT: A 270 MET cc_start: 0.6015 (tpp) cc_final: 0.5677 (tpt) REVERT: A 343 LYS cc_start: 0.5108 (tmtp) cc_final: 0.4903 (tptp) REVERT: A 344 ARG cc_start: 0.7754 (mpp-170) cc_final: 0.7104 (ttp80) REVERT: A 383 LYS cc_start: 0.6399 (pttt) cc_final: 0.6179 (ptpt) REVERT: A 387 GLU cc_start: 0.5014 (tp30) cc_final: 0.4476 (tm-30) REVERT: A 389 GLU cc_start: 0.7323 (tp30) cc_final: 0.6769 (mt-10) REVERT: A 444 GLU cc_start: 0.7932 (pm20) cc_final: 0.7338 (mt-10) REVERT: A 445 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7326 (tp30) REVERT: A 481 GLU cc_start: 0.5667 (mp0) cc_final: 0.5094 (mp0) REVERT: A 545 PHE cc_start: 0.6062 (m-80) cc_final: 0.5851 (m-80) REVERT: A 626 GLU cc_start: 0.6189 (pt0) cc_final: 0.5978 (pp20) REVERT: A 676 ARG cc_start: 0.6976 (mtt-85) cc_final: 0.6597 (mmm-85) REVERT: A 1128 LEU cc_start: 0.5464 (mt) cc_final: 0.5240 (mt) REVERT: A 1132 ARG cc_start: 0.5791 (ttp-170) cc_final: 0.5010 (mtt-85) REVERT: A 1161 MET cc_start: 0.4885 (mmm) cc_final: 0.4579 (mmt) REVERT: B 107 LYS cc_start: 0.6813 (mttm) cc_final: 0.6517 (pttp) REVERT: B 112 LEU cc_start: 0.6189 (tt) cc_final: 0.5955 (tt) REVERT: B 158 MET cc_start: 0.6497 (ttm) cc_final: 0.6289 (tpp) REVERT: B 184 MET cc_start: 0.5134 (mpp) cc_final: 0.4875 (mtm) REVERT: B 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6990 (t0) REVERT: B 260 THR cc_start: 0.7688 (p) cc_final: 0.7476 (p) REVERT: B 270 MET cc_start: 0.6021 (tpp) cc_final: 0.5677 (tpt) REVERT: B 343 LYS cc_start: 0.5091 (tmtp) cc_final: 0.4886 (tptp) REVERT: B 344 ARG cc_start: 0.7732 (mpp-170) cc_final: 0.7100 (ttp80) REVERT: B 383 LYS cc_start: 0.6395 (pttt) cc_final: 0.6175 (ptpt) REVERT: B 387 GLU cc_start: 0.5017 (tp30) cc_final: 0.4479 (tm-30) REVERT: B 389 GLU cc_start: 0.7324 (tp30) cc_final: 0.6769 (mt-10) REVERT: B 444 GLU cc_start: 0.7910 (pm20) cc_final: 0.7308 (mt-10) REVERT: B 445 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7316 (tp30) REVERT: B 481 GLU cc_start: 0.5690 (mp0) cc_final: 0.5093 (mp0) REVERT: B 490 LYS cc_start: 0.5820 (ttmp) cc_final: 0.5611 (tttp) REVERT: B 533 MET cc_start: 0.6928 (mtp) cc_final: 0.6723 (mmm) REVERT: B 670 GLU cc_start: 0.6685 (tt0) cc_final: 0.5896 (tm-30) REVERT: B 676 ARG cc_start: 0.6979 (mtt-85) cc_final: 0.6017 (mtm110) REVERT: B 1128 LEU cc_start: 0.5440 (mt) cc_final: 0.5210 (mt) REVERT: B 1132 ARG cc_start: 0.5817 (ttp-170) cc_final: 0.5029 (mtt-85) REVERT: B 1161 MET cc_start: 0.4897 (mmm) cc_final: 0.4585 (mmt) REVERT: C 107 LYS cc_start: 0.6748 (mttm) cc_final: 0.6461 (pttp) REVERT: C 112 LEU cc_start: 0.6190 (tt) cc_final: 0.5963 (tt) REVERT: C 158 MET cc_start: 0.6403 (ttm) cc_final: 0.6173 (tpp) REVERT: C 184 MET cc_start: 0.5140 (mpp) cc_final: 0.4882 (mtm) REVERT: C 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6983 (t0) REVERT: C 260 THR cc_start: 0.7691 (p) cc_final: 0.7480 (p) REVERT: C 270 MET cc_start: 0.5984 (tpp) cc_final: 0.5444 (tpt) REVERT: C 343 LYS cc_start: 0.5066 (tmtp) cc_final: 0.4858 (tptp) REVERT: C 344 ARG cc_start: 0.7733 (mpp-170) cc_final: 0.7100 (ttp80) REVERT: C 383 LYS cc_start: 0.6405 (pttt) cc_final: 0.6187 (ptpt) REVERT: C 387 GLU cc_start: 0.5022 (tp30) cc_final: 0.4486 (tm-30) REVERT: C 389 GLU cc_start: 0.7348 (tp30) cc_final: 0.6767 (mt-10) REVERT: C 444 GLU cc_start: 0.7911 (pm20) cc_final: 0.7309 (mt-10) REVERT: C 445 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7304 (tp30) REVERT: C 481 GLU cc_start: 0.5774 (mp0) cc_final: 0.5163 (mp0) REVERT: C 490 LYS cc_start: 0.5826 (ttmp) cc_final: 0.5615 (tttp) REVERT: C 676 ARG cc_start: 0.7003 (mtt-85) cc_final: 0.6155 (mtm110) REVERT: C 1053 GLU cc_start: 0.6762 (pt0) cc_final: 0.6328 (mt-10) REVERT: C 1128 LEU cc_start: 0.5332 (mt) cc_final: 0.5111 (mt) REVERT: C 1132 ARG cc_start: 0.5749 (ttp-170) cc_final: 0.5015 (mtt-85) REVERT: C 1161 MET cc_start: 0.4858 (mmm) cc_final: 0.4534 (mmt) REVERT: D 107 LYS cc_start: 0.6743 (mttm) cc_final: 0.6441 (pttp) REVERT: D 112 LEU cc_start: 0.6279 (tt) cc_final: 0.6072 (tt) REVERT: D 158 MET cc_start: 0.6501 (ttm) cc_final: 0.6293 (tpp) REVERT: D 184 MET cc_start: 0.5137 (mpp) cc_final: 0.4873 (mtm) REVERT: D 220 ASP cc_start: 0.7314 (t70) cc_final: 0.7031 (t0) REVERT: D 260 THR cc_start: 0.7684 (p) cc_final: 0.7471 (p) REVERT: D 270 MET cc_start: 0.6032 (tpp) cc_final: 0.5685 (tpt) REVERT: D 343 LYS cc_start: 0.5101 (tmtp) cc_final: 0.4895 (tptp) REVERT: D 344 ARG cc_start: 0.7749 (mpp-170) cc_final: 0.7108 (ttp80) REVERT: D 383 LYS cc_start: 0.6410 (pttt) cc_final: 0.6191 (ptpt) REVERT: D 387 GLU cc_start: 0.5022 (tp30) cc_final: 0.4485 (tm-30) REVERT: D 389 GLU cc_start: 0.7340 (tp30) cc_final: 0.6761 (mt-10) REVERT: D 444 GLU cc_start: 0.7921 (pm20) cc_final: 0.7328 (mt-10) REVERT: D 445 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7314 (tp30) REVERT: D 481 GLU cc_start: 0.5757 (mp0) cc_final: 0.5177 (mp0) REVERT: D 490 LYS cc_start: 0.5833 (ttmp) cc_final: 0.5622 (tttp) REVERT: D 626 GLU cc_start: 0.6201 (pt0) cc_final: 0.5988 (pp20) REVERT: D 676 ARG cc_start: 0.7000 (mtt-85) cc_final: 0.6635 (mmm-85) REVERT: D 1128 LEU cc_start: 0.5334 (mt) cc_final: 0.5115 (mt) REVERT: D 1132 ARG cc_start: 0.5776 (ttp-170) cc_final: 0.5040 (mtt-85) REVERT: D 1161 MET cc_start: 0.4899 (mmm) cc_final: 0.4575 (mmt) outliers start: 12 outliers final: 4 residues processed: 791 average time/residue: 0.5291 time to fit residues: 644.7079 Evaluate side-chains 458 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 454 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain D residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 178 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 332 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 385 optimal weight: 0.4980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 GLN B 513 GLN C 513 GLN D 513 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4978 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35924 Z= 0.216 Angle : 0.586 8.697 48328 Z= 0.298 Chirality : 0.042 0.154 5376 Planarity : 0.004 0.052 5992 Dihedral : 12.540 88.603 6076 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 0.78 % Allowed : 7.64 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.55 (0.12), residues: 4196 helix: 0.81 (0.10), residues: 2544 sheet: -1.31 (0.30), residues: 208 loop : -2.38 (0.14), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 705 HIS 0.003 0.001 HIS B 250 PHE 0.014 0.001 PHE D 584 TYR 0.023 0.001 TYR D 312 ARG 0.005 0.001 ARG D1194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 493 time to evaluate : 4.271 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.5869 (mtm) cc_final: 0.5341 (mtp) REVERT: A 220 ASP cc_start: 0.7116 (t70) cc_final: 0.6737 (t0) REVERT: A 279 MET cc_start: 0.6544 (mtm) cc_final: 0.6326 (mtt) REVERT: A 343 LYS cc_start: 0.5070 (tmtp) cc_final: 0.4853 (tptp) REVERT: A 344 ARG cc_start: 0.7831 (mpp-170) cc_final: 0.7230 (ttp80) REVERT: A 383 LYS cc_start: 0.6594 (pttt) cc_final: 0.6276 (ptpt) REVERT: A 387 GLU cc_start: 0.5094 (tp30) cc_final: 0.4655 (tm-30) REVERT: A 444 GLU cc_start: 0.7936 (pm20) cc_final: 0.7350 (mt-10) REVERT: A 1132 ARG cc_start: 0.5842 (ttp-170) cc_final: 0.5107 (mtt-85) REVERT: B 197 MET cc_start: 0.5850 (mtm) cc_final: 0.5320 (mtp) REVERT: B 220 ASP cc_start: 0.7095 (t70) cc_final: 0.6703 (t0) REVERT: B 279 MET cc_start: 0.6570 (mtm) cc_final: 0.6350 (mtt) REVERT: B 343 LYS cc_start: 0.5067 (tmtp) cc_final: 0.4848 (tptp) REVERT: B 344 ARG cc_start: 0.7788 (mpp-170) cc_final: 0.7163 (ttp80) REVERT: B 383 LYS cc_start: 0.6533 (pttt) cc_final: 0.6246 (ptpt) REVERT: B 387 GLU cc_start: 0.5096 (tp30) cc_final: 0.4657 (tm-30) REVERT: B 444 GLU cc_start: 0.7958 (pm20) cc_final: 0.7352 (mt-10) REVERT: B 530 MET cc_start: 0.4707 (mtp) cc_final: 0.4480 (mtp) REVERT: B 1132 ARG cc_start: 0.5863 (ttp-170) cc_final: 0.5109 (mtt-85) REVERT: C 197 MET cc_start: 0.5852 (mtm) cc_final: 0.5320 (mtp) REVERT: C 220 ASP cc_start: 0.7079 (t70) cc_final: 0.6685 (t0) REVERT: C 279 MET cc_start: 0.6551 (mtm) cc_final: 0.6315 (mtt) REVERT: C 343 LYS cc_start: 0.5063 (tmtp) cc_final: 0.4844 (tptp) REVERT: C 344 ARG cc_start: 0.7792 (mpp-170) cc_final: 0.7178 (ttp80) REVERT: C 383 LYS cc_start: 0.6492 (pttt) cc_final: 0.6177 (ptpt) REVERT: C 387 GLU cc_start: 0.5053 (tp30) cc_final: 0.4609 (tm-30) REVERT: C 392 ILE cc_start: 0.7452 (tp) cc_final: 0.7250 (tp) REVERT: C 444 GLU cc_start: 0.7960 (pm20) cc_final: 0.7353 (mt-10) REVERT: C 530 MET cc_start: 0.4705 (mtp) cc_final: 0.4475 (mtp) REVERT: C 1132 ARG cc_start: 0.5838 (ttp-170) cc_final: 0.5088 (mmt180) REVERT: D 197 MET cc_start: 0.5862 (mtm) cc_final: 0.5335 (mtp) REVERT: D 220 ASP cc_start: 0.7138 (t70) cc_final: 0.6748 (t0) REVERT: D 279 MET cc_start: 0.6525 (mtm) cc_final: 0.6289 (mtt) REVERT: D 343 LYS cc_start: 0.5065 (tmtp) cc_final: 0.4846 (tptp) REVERT: D 344 ARG cc_start: 0.7788 (mpp-170) cc_final: 0.7168 (ttp80) REVERT: D 383 LYS cc_start: 0.6467 (pttt) cc_final: 0.6187 (ptpt) REVERT: D 387 GLU cc_start: 0.5116 (tp30) cc_final: 0.4649 (tm-30) REVERT: D 392 ILE cc_start: 0.7486 (tp) cc_final: 0.7244 (tp) REVERT: D 444 GLU cc_start: 0.7957 (pm20) cc_final: 0.7357 (mt-10) REVERT: D 1132 ARG cc_start: 0.5862 (ttp-170) cc_final: 0.5113 (mtt-85) outliers start: 28 outliers final: 20 residues processed: 508 average time/residue: 0.5333 time to fit residues: 421.9600 Evaluate side-chains 464 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 444 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 479 MET Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 1034 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 213 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 320 optimal weight: 50.0000 chunk 262 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 385 optimal weight: 0.0050 chunk 416 optimal weight: 8.9990 chunk 343 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS A1086 ASN B 250 HIS B 983 GLN B1086 ASN C 250 HIS C 983 GLN C1086 ASN D 250 HIS D 983 GLN D1086 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4980 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35924 Z= 0.269 Angle : 0.563 6.751 48328 Z= 0.287 Chirality : 0.042 0.179 5376 Planarity : 0.005 0.046 5992 Dihedral : 11.264 87.043 6076 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 2.00 % Allowed : 7.64 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.14 (0.13), residues: 4196 helix: 1.05 (0.10), residues: 2568 sheet: -1.26 (0.30), residues: 256 loop : -2.09 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 705 HIS 0.004 0.001 HIS B 250 PHE 0.016 0.001 PHE D 584 TYR 0.015 0.002 TYR C 229 ARG 0.005 0.001 ARG B1194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 435 time to evaluate : 4.058 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.5914 (mtm) cc_final: 0.5395 (mtp) REVERT: A 220 ASP cc_start: 0.7205 (t70) cc_final: 0.6792 (t0) REVERT: A 343 LYS cc_start: 0.5063 (tmtp) cc_final: 0.4789 (tptp) REVERT: A 344 ARG cc_start: 0.7799 (mpp-170) cc_final: 0.7078 (ttp-110) REVERT: A 383 LYS cc_start: 0.6654 (pttt) cc_final: 0.6402 (ptpt) REVERT: A 387 GLU cc_start: 0.5021 (tp30) cc_final: 0.4477 (tm-30) REVERT: A 389 GLU cc_start: 0.6845 (tp30) cc_final: 0.6413 (mt-10) REVERT: A 444 GLU cc_start: 0.7962 (pm20) cc_final: 0.7356 (mt-10) REVERT: A 1132 ARG cc_start: 0.5879 (ttp-170) cc_final: 0.5127 (mtt-85) REVERT: B 197 MET cc_start: 0.5885 (mtm) cc_final: 0.5360 (mtp) REVERT: B 220 ASP cc_start: 0.7200 (t70) cc_final: 0.6787 (t0) REVERT: B 343 LYS cc_start: 0.5062 (tmtp) cc_final: 0.4786 (tptp) REVERT: B 344 ARG cc_start: 0.7800 (mpp-170) cc_final: 0.7074 (ttp-110) REVERT: B 383 LYS cc_start: 0.6650 (pttt) cc_final: 0.6398 (ptpt) REVERT: B 387 GLU cc_start: 0.5025 (tp30) cc_final: 0.4479 (tm-30) REVERT: B 389 GLU cc_start: 0.6866 (tp30) cc_final: 0.6423 (mt-10) REVERT: B 444 GLU cc_start: 0.7963 (pm20) cc_final: 0.7355 (mt-10) REVERT: B 1132 ARG cc_start: 0.5886 (ttp-170) cc_final: 0.5129 (mtt-85) REVERT: C 197 MET cc_start: 0.5907 (mtm) cc_final: 0.5373 (mtp) REVERT: C 220 ASP cc_start: 0.7118 (t70) cc_final: 0.6725 (t0) REVERT: C 344 ARG cc_start: 0.7801 (mpp-170) cc_final: 0.7188 (ttp-110) REVERT: C 383 LYS cc_start: 0.6592 (pttt) cc_final: 0.6333 (ptpt) REVERT: C 387 GLU cc_start: 0.5026 (tp30) cc_final: 0.4549 (tm-30) REVERT: C 444 GLU cc_start: 0.7964 (pm20) cc_final: 0.7356 (mt-10) REVERT: C 1053 GLU cc_start: 0.7217 (pt0) cc_final: 0.6532 (mt-10) REVERT: C 1132 ARG cc_start: 0.5918 (ttp-170) cc_final: 0.5176 (mtt-85) REVERT: D 197 MET cc_start: 0.5904 (mtm) cc_final: 0.5375 (mtp) REVERT: D 220 ASP cc_start: 0.7207 (t70) cc_final: 0.6795 (t0) REVERT: D 344 ARG cc_start: 0.7799 (mpp-170) cc_final: 0.7191 (ttp-110) REVERT: D 383 LYS cc_start: 0.6474 (pttt) cc_final: 0.6151 (ptpt) REVERT: D 387 GLU cc_start: 0.5178 (tp30) cc_final: 0.4713 (tm-30) REVERT: D 444 GLU cc_start: 0.7961 (pm20) cc_final: 0.7361 (mt-10) REVERT: D 1132 ARG cc_start: 0.5877 (ttp-170) cc_final: 0.5124 (mtt-85) outliers start: 72 outliers final: 38 residues processed: 484 average time/residue: 0.5089 time to fit residues: 387.2861 Evaluate side-chains 458 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 420 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 620 MET Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 381 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 259 optimal weight: 1.9990 chunk 387 optimal weight: 3.9990 chunk 409 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 110 optimal weight: 0.0770 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 983 GLN C 983 GLN D 983 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4976 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35924 Z= 0.249 Angle : 0.537 9.147 48328 Z= 0.273 Chirality : 0.042 0.185 5376 Planarity : 0.004 0.043 5992 Dihedral : 10.861 84.332 6076 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 1.78 % Allowed : 9.00 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.03 (0.13), residues: 4196 helix: 1.17 (0.10), residues: 2580 sheet: -1.22 (0.31), residues: 260 loop : -2.00 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 705 HIS 0.007 0.001 HIS D 250 PHE 0.014 0.001 PHE A 584 TYR 0.015 0.002 TYR D 312 ARG 0.004 0.000 ARG C1194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 427 time to evaluate : 3.970 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.6032 (mtm) cc_final: 0.5539 (mtp) REVERT: A 220 ASP cc_start: 0.7256 (t70) cc_final: 0.6839 (t0) REVERT: A 344 ARG cc_start: 0.7762 (mpp-170) cc_final: 0.7059 (ttp-110) REVERT: A 383 LYS cc_start: 0.6675 (pttt) cc_final: 0.6206 (ptpt) REVERT: A 389 GLU cc_start: 0.6797 (tp30) cc_final: 0.6355 (mt-10) REVERT: A 444 GLU cc_start: 0.8001 (pm20) cc_final: 0.7407 (mt-10) REVERT: A 1053 GLU cc_start: 0.6862 (pt0) cc_final: 0.6509 (mt-10) REVERT: A 1132 ARG cc_start: 0.5866 (ttp-170) cc_final: 0.5132 (mtt-85) REVERT: B 197 MET cc_start: 0.6031 (mtm) cc_final: 0.5537 (mtp) REVERT: B 220 ASP cc_start: 0.7256 (t70) cc_final: 0.6839 (t0) REVERT: B 344 ARG cc_start: 0.7763 (mpp-170) cc_final: 0.7056 (ttp-110) REVERT: B 383 LYS cc_start: 0.6672 (pttt) cc_final: 0.6203 (ptpt) REVERT: B 389 GLU cc_start: 0.6807 (tp30) cc_final: 0.6372 (mt-10) REVERT: B 444 GLU cc_start: 0.8005 (pm20) cc_final: 0.7411 (mt-10) REVERT: B 1053 GLU cc_start: 0.6822 (pt0) cc_final: 0.6445 (mt-10) REVERT: B 1132 ARG cc_start: 0.5864 (ttp-170) cc_final: 0.5127 (mtt-85) REVERT: C 197 MET cc_start: 0.6030 (mtm) cc_final: 0.5533 (mtp) REVERT: C 220 ASP cc_start: 0.7262 (t70) cc_final: 0.6845 (t0) REVERT: C 344 ARG cc_start: 0.7764 (mpp-170) cc_final: 0.7056 (ttp-110) REVERT: C 383 LYS cc_start: 0.6720 (pttt) cc_final: 0.6483 (ptpt) REVERT: C 387 GLU cc_start: 0.4948 (tp30) cc_final: 0.4369 (tm-30) REVERT: C 389 GLU cc_start: 0.6791 (tp30) cc_final: 0.6374 (mt-10) REVERT: C 444 GLU cc_start: 0.8006 (pm20) cc_final: 0.7403 (mt-10) REVERT: C 1053 GLU cc_start: 0.7180 (pt0) cc_final: 0.6547 (mt-10) REVERT: C 1132 ARG cc_start: 0.5917 (ttp-170) cc_final: 0.5165 (mtt-85) REVERT: D 197 MET cc_start: 0.6027 (mtm) cc_final: 0.5535 (mtp) REVERT: D 220 ASP cc_start: 0.7266 (t70) cc_final: 0.6848 (t0) REVERT: D 344 ARG cc_start: 0.7762 (mpp-170) cc_final: 0.7059 (ttp-110) REVERT: D 383 LYS cc_start: 0.6475 (pttt) cc_final: 0.6002 (ptpt) REVERT: D 389 GLU cc_start: 0.6804 (tp30) cc_final: 0.6367 (mt-10) REVERT: D 444 GLU cc_start: 0.7999 (pm20) cc_final: 0.7412 (mt-10) REVERT: D 1132 ARG cc_start: 0.5874 (ttp-170) cc_final: 0.5120 (mtt-85) outliers start: 64 outliers final: 46 residues processed: 478 average time/residue: 0.5535 time to fit residues: 419.6920 Evaluate side-chains 454 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 408 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 341 optimal weight: 6.9990 chunk 232 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 349 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 209 optimal weight: 0.9990 chunk 367 optimal weight: 0.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B 983 GLN C 844 ASN C 983 GLN D 983 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4976 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35924 Z= 0.248 Angle : 0.525 7.783 48328 Z= 0.266 Chirality : 0.041 0.158 5376 Planarity : 0.004 0.040 5992 Dihedral : 10.502 74.680 6076 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.14 % Allowed : 9.64 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.13 (0.13), residues: 4196 helix: 1.24 (0.10), residues: 2580 sheet: -1.20 (0.31), residues: 260 loop : -1.95 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 705 HIS 0.004 0.001 HIS C 250 PHE 0.014 0.001 PHE B 584 TYR 0.010 0.001 TYR C 229 ARG 0.007 0.001 ARG D 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 416 time to evaluate : 3.932 Fit side-chains REVERT: A 197 MET cc_start: 0.6144 (mtm) cc_final: 0.5642 (mtp) REVERT: A 220 ASP cc_start: 0.7244 (t70) cc_final: 0.6814 (t0) REVERT: A 344 ARG cc_start: 0.7771 (mpp-170) cc_final: 0.7055 (ttp-110) REVERT: A 383 LYS cc_start: 0.6444 (pttt) cc_final: 0.6171 (ptpt) REVERT: A 389 GLU cc_start: 0.6805 (tp30) cc_final: 0.6388 (mt-10) REVERT: A 444 GLU cc_start: 0.8006 (pm20) cc_final: 0.7397 (mt-10) REVERT: A 1053 GLU cc_start: 0.6752 (pt0) cc_final: 0.6421 (mt-10) REVERT: A 1132 ARG cc_start: 0.5897 (ttp-170) cc_final: 0.5158 (mtt-85) REVERT: B 197 MET cc_start: 0.6146 (mtm) cc_final: 0.5643 (mtp) REVERT: B 220 ASP cc_start: 0.7242 (t70) cc_final: 0.6812 (t0) REVERT: B 344 ARG cc_start: 0.7771 (mpp-170) cc_final: 0.7052 (ttp-110) REVERT: B 383 LYS cc_start: 0.6442 (pttt) cc_final: 0.6153 (ptpt) REVERT: B 389 GLU cc_start: 0.6811 (tp30) cc_final: 0.6395 (mt-10) REVERT: B 444 GLU cc_start: 0.8009 (pm20) cc_final: 0.7408 (mt-10) REVERT: B 480 ARG cc_start: 0.6673 (mtp-110) cc_final: 0.6453 (mtp-110) REVERT: B 1053 GLU cc_start: 0.6832 (pt0) cc_final: 0.6505 (mt-10) REVERT: B 1132 ARG cc_start: 0.5901 (ttp-170) cc_final: 0.5161 (mtt-85) REVERT: C 197 MET cc_start: 0.6139 (mtm) cc_final: 0.5632 (mtp) REVERT: C 220 ASP cc_start: 0.7248 (t70) cc_final: 0.6817 (t0) REVERT: C 344 ARG cc_start: 0.7768 (mpp-170) cc_final: 0.7055 (ttp-110) REVERT: C 383 LYS cc_start: 0.6446 (pttt) cc_final: 0.5973 (ptpt) REVERT: C 389 GLU cc_start: 0.6793 (tp30) cc_final: 0.6371 (mt-10) REVERT: C 444 GLU cc_start: 0.8009 (pm20) cc_final: 0.7391 (mt-10) REVERT: C 480 ARG cc_start: 0.6673 (mtp-110) cc_final: 0.6454 (mtp-110) REVERT: C 1053 GLU cc_start: 0.7168 (pt0) cc_final: 0.6626 (mt-10) REVERT: C 1132 ARG cc_start: 0.5966 (ttp-170) cc_final: 0.5215 (mtt-85) REVERT: D 197 MET cc_start: 0.6138 (mtm) cc_final: 0.5640 (mtp) REVERT: D 220 ASP cc_start: 0.7252 (t70) cc_final: 0.6819 (t0) REVERT: D 344 ARG cc_start: 0.7770 (mpp-170) cc_final: 0.7054 (ttp-110) REVERT: D 383 LYS cc_start: 0.6296 (pttt) cc_final: 0.5971 (ptpt) REVERT: D 389 GLU cc_start: 0.6827 (tp30) cc_final: 0.6374 (mt-10) REVERT: D 444 GLU cc_start: 0.8008 (pm20) cc_final: 0.7397 (mt-10) REVERT: D 480 ARG cc_start: 0.6674 (mtp-110) cc_final: 0.6459 (mtp-110) REVERT: D 1053 GLU cc_start: 0.7000 (pt0) cc_final: 0.6568 (mt-10) REVERT: D 1132 ARG cc_start: 0.5926 (ttp-170) cc_final: 0.5171 (mtt-85) outliers start: 77 outliers final: 41 residues processed: 477 average time/residue: 0.5071 time to fit residues: 380.7359 Evaluate side-chains 448 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 407 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 396 SER Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 137 optimal weight: 2.9990 chunk 369 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 410 optimal weight: 0.0010 chunk 340 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN B 844 ASN B 983 GLN C 844 ASN C 983 GLN D 844 ASN D 983 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4974 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35924 Z= 0.233 Angle : 0.513 7.738 48328 Z= 0.260 Chirality : 0.041 0.157 5376 Planarity : 0.004 0.040 5992 Dihedral : 10.255 66.603 6072 Min Nonbonded Distance : 1.635 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.45 % Rotamer: Outliers : 2.22 % Allowed : 9.75 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.27 (0.13), residues: 4196 helix: 1.36 (0.10), residues: 2576 sheet: -1.04 (0.31), residues: 256 loop : -1.90 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 705 HIS 0.004 0.001 HIS C 250 PHE 0.012 0.001 PHE C 584 TYR 0.009 0.001 TYR A 229 ARG 0.005 0.000 ARG B1194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 408 time to evaluate : 4.059 Fit side-chains REVERT: A 193 GLU cc_start: 0.7252 (pt0) cc_final: 0.6905 (pp20) REVERT: A 197 MET cc_start: 0.6138 (mtm) cc_final: 0.5392 (mtp) REVERT: A 220 ASP cc_start: 0.7300 (t70) cc_final: 0.6884 (t0) REVERT: A 344 ARG cc_start: 0.7780 (mpp-170) cc_final: 0.7060 (ttp-110) REVERT: A 383 LYS cc_start: 0.6319 (pttt) cc_final: 0.5964 (ptpt) REVERT: A 389 GLU cc_start: 0.6799 (tp30) cc_final: 0.6385 (mt-10) REVERT: A 444 GLU cc_start: 0.8008 (pm20) cc_final: 0.7389 (mt-10) REVERT: A 1053 GLU cc_start: 0.6736 (pt0) cc_final: 0.6493 (mt-10) REVERT: A 1132 ARG cc_start: 0.5936 (ttp-170) cc_final: 0.5200 (mtt-85) REVERT: B 193 GLU cc_start: 0.7253 (pt0) cc_final: 0.6904 (pp20) REVERT: B 197 MET cc_start: 0.6135 (mtm) cc_final: 0.5389 (mtp) REVERT: B 220 ASP cc_start: 0.7274 (t70) cc_final: 0.6843 (t0) REVERT: B 344 ARG cc_start: 0.7781 (mpp-170) cc_final: 0.7058 (ttp-110) REVERT: B 383 LYS cc_start: 0.6511 (pttt) cc_final: 0.6231 (ptpt) REVERT: B 389 GLU cc_start: 0.6799 (tp30) cc_final: 0.6377 (mt-10) REVERT: B 444 GLU cc_start: 0.8025 (pm20) cc_final: 0.7426 (mt-10) REVERT: B 1053 GLU cc_start: 0.6821 (pt0) cc_final: 0.6576 (mt-10) REVERT: B 1132 ARG cc_start: 0.5968 (ttp-170) cc_final: 0.5213 (mtt-85) REVERT: C 197 MET cc_start: 0.6133 (mtm) cc_final: 0.5630 (mtp) REVERT: C 220 ASP cc_start: 0.7234 (t70) cc_final: 0.6810 (t0) REVERT: C 344 ARG cc_start: 0.7777 (mpp-170) cc_final: 0.7133 (ttp-110) REVERT: C 383 LYS cc_start: 0.6348 (pttt) cc_final: 0.6003 (ptpt) REVERT: C 444 GLU cc_start: 0.8023 (pm20) cc_final: 0.7418 (mt-10) REVERT: C 480 ARG cc_start: 0.6705 (mtp-110) cc_final: 0.6493 (mtp-110) REVERT: C 1053 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6562 (mt-10) REVERT: C 1132 ARG cc_start: 0.5982 (ttp-170) cc_final: 0.5212 (mtt-85) REVERT: D 193 GLU cc_start: 0.7206 (pt0) cc_final: 0.6876 (pp20) REVERT: D 197 MET cc_start: 0.6134 (mtm) cc_final: 0.5385 (mtp) REVERT: D 220 ASP cc_start: 0.7304 (t70) cc_final: 0.6885 (t0) REVERT: D 344 ARG cc_start: 0.7779 (mpp-170) cc_final: 0.7136 (ttp-110) REVERT: D 383 LYS cc_start: 0.6203 (pttt) cc_final: 0.5856 (ptpt) REVERT: D 444 GLU cc_start: 0.8021 (pm20) cc_final: 0.7422 (mt-10) REVERT: D 480 ARG cc_start: 0.6706 (mtp-110) cc_final: 0.6494 (mtp-110) REVERT: D 1053 GLU cc_start: 0.6978 (pt0) cc_final: 0.6592 (mt-10) REVERT: D 1132 ARG cc_start: 0.5961 (ttp-170) cc_final: 0.5208 (mtt-85) outliers start: 80 outliers final: 56 residues processed: 471 average time/residue: 0.5463 time to fit residues: 411.7355 Evaluate side-chains 461 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 404 time to evaluate : 3.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1095 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1107 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 395 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 299 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 408 optimal weight: 0.0060 chunk 255 optimal weight: 0.8980 chunk 249 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN B 844 ASN ** B 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4984 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35924 Z= 0.314 Angle : 0.560 7.640 48328 Z= 0.284 Chirality : 0.043 0.168 5376 Planarity : 0.005 0.043 5992 Dihedral : 10.551 65.763 6072 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 2.03 % Allowed : 10.72 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 4196 helix: 1.21 (0.10), residues: 2572 sheet: -1.01 (0.32), residues: 256 loop : -1.83 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 705 HIS 0.004 0.001 HIS C 250 PHE 0.014 0.001 PHE B 584 TYR 0.013 0.002 TYR A 229 ARG 0.007 0.001 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 427 time to evaluate : 3.729 Fit side-chains REVERT: A 193 GLU cc_start: 0.7120 (pt0) cc_final: 0.6835 (pp20) REVERT: A 197 MET cc_start: 0.6099 (mtm) cc_final: 0.5602 (mtp) REVERT: A 220 ASP cc_start: 0.7258 (t70) cc_final: 0.6855 (t0) REVERT: A 344 ARG cc_start: 0.7756 (mpp-170) cc_final: 0.6995 (ttp-110) REVERT: A 383 LYS cc_start: 0.6375 (pttt) cc_final: 0.6043 (ptpt) REVERT: A 389 GLU cc_start: 0.6821 (tp30) cc_final: 0.6381 (mt-10) REVERT: A 444 GLU cc_start: 0.7935 (pm20) cc_final: 0.7393 (mt-10) REVERT: A 477 LEU cc_start: 0.4096 (OUTLIER) cc_final: 0.3776 (tm) REVERT: A 676 ARG cc_start: 0.7046 (mpp80) cc_final: 0.6416 (mmm-85) REVERT: A 1132 ARG cc_start: 0.5890 (ttp-170) cc_final: 0.5095 (mtt-85) REVERT: B 193 GLU cc_start: 0.7115 (pt0) cc_final: 0.6822 (pp20) REVERT: B 197 MET cc_start: 0.6100 (mtm) cc_final: 0.5604 (mtp) REVERT: B 220 ASP cc_start: 0.7257 (t70) cc_final: 0.6855 (t0) REVERT: B 344 ARG cc_start: 0.7755 (mpp-170) cc_final: 0.7031 (ttp-110) REVERT: B 383 LYS cc_start: 0.6178 (pttt) cc_final: 0.5828 (ptpt) REVERT: B 389 GLU cc_start: 0.6815 (tp30) cc_final: 0.6384 (mt-10) REVERT: B 444 GLU cc_start: 0.7973 (pm20) cc_final: 0.7419 (mt-10) REVERT: B 477 LEU cc_start: 0.4101 (OUTLIER) cc_final: 0.3748 (tm) REVERT: B 676 ARG cc_start: 0.7052 (mpp80) cc_final: 0.6394 (mmm-85) REVERT: B 1053 GLU cc_start: 0.6697 (pt0) cc_final: 0.6478 (mt-10) REVERT: B 1132 ARG cc_start: 0.5893 (ttp-170) cc_final: 0.5089 (mtt-85) REVERT: C 193 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7106 (pp20) REVERT: C 197 MET cc_start: 0.6103 (mtm) cc_final: 0.5600 (mtp) REVERT: C 220 ASP cc_start: 0.7230 (t70) cc_final: 0.6830 (t0) REVERT: C 344 ARG cc_start: 0.7754 (mpp-170) cc_final: 0.7105 (ttp-110) REVERT: C 383 LYS cc_start: 0.6047 (pttt) cc_final: 0.5667 (ptpt) REVERT: C 444 GLU cc_start: 0.7973 (pm20) cc_final: 0.7414 (mt-10) REVERT: C 477 LEU cc_start: 0.4102 (OUTLIER) cc_final: 0.3750 (tm) REVERT: C 676 ARG cc_start: 0.7073 (mpp80) cc_final: 0.6432 (mmm-85) REVERT: C 1053 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: C 1132 ARG cc_start: 0.5981 (ttp-170) cc_final: 0.5235 (mtt-85) REVERT: D 193 GLU cc_start: 0.7059 (pt0) cc_final: 0.6757 (pp20) REVERT: D 197 MET cc_start: 0.6107 (mtm) cc_final: 0.5605 (mtp) REVERT: D 220 ASP cc_start: 0.7263 (t70) cc_final: 0.6857 (t0) REVERT: D 344 ARG cc_start: 0.7756 (mpp-170) cc_final: 0.7107 (ttp-110) REVERT: D 383 LYS cc_start: 0.6193 (pttt) cc_final: 0.5838 (ptpt) REVERT: D 444 GLU cc_start: 0.7933 (pm20) cc_final: 0.7396 (mt-10) REVERT: D 477 LEU cc_start: 0.4167 (OUTLIER) cc_final: 0.3816 (tm) REVERT: D 676 ARG cc_start: 0.7055 (mpp80) cc_final: 0.6422 (mmm-85) REVERT: D 1053 GLU cc_start: 0.6963 (pt0) cc_final: 0.6589 (mt-10) REVERT: D 1132 ARG cc_start: 0.5953 (ttp-170) cc_final: 0.5159 (mtt-85) outliers start: 73 outliers final: 56 residues processed: 479 average time/residue: 0.5065 time to fit residues: 384.0252 Evaluate side-chains 481 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 419 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 752 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1095 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 160 ARG Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 752 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1107 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 252 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 259 optimal weight: 0.7980 chunk 278 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 321 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN A 963 GLN B 844 ASN B 963 GLN ** B 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN C 983 GLN D 844 ASN ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4969 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35924 Z= 0.186 Angle : 0.488 7.426 48328 Z= 0.250 Chirality : 0.040 0.154 5376 Planarity : 0.004 0.040 5992 Dihedral : 10.067 60.442 6072 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 1.61 % Allowed : 11.42 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.46 (0.13), residues: 4196 helix: 1.50 (0.10), residues: 2572 sheet: -1.22 (0.31), residues: 268 loop : -1.73 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 705 HIS 0.003 0.001 HIS D 250 PHE 0.009 0.001 PHE B 584 TYR 0.017 0.001 TYR C 312 ARG 0.007 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 425 time to evaluate : 3.986 Fit side-chains REVERT: A 197 MET cc_start: 0.6058 (mtm) cc_final: 0.5688 (mtp) REVERT: A 220 ASP cc_start: 0.7255 (t70) cc_final: 0.6823 (t0) REVERT: A 344 ARG cc_start: 0.7738 (mpp-170) cc_final: 0.6967 (ttp-110) REVERT: A 383 LYS cc_start: 0.6308 (pttt) cc_final: 0.5967 (ptpt) REVERT: A 389 GLU cc_start: 0.6973 (tp30) cc_final: 0.6532 (mt-10) REVERT: A 444 GLU cc_start: 0.7983 (pm20) cc_final: 0.7403 (mt-10) REVERT: A 477 LEU cc_start: 0.4091 (OUTLIER) cc_final: 0.3758 (tm) REVERT: A 676 ARG cc_start: 0.7086 (mpp80) cc_final: 0.6440 (mmm-85) REVERT: A 1132 ARG cc_start: 0.5928 (ttp-170) cc_final: 0.5150 (mtt-85) REVERT: B 197 MET cc_start: 0.6057 (mtm) cc_final: 0.5689 (mtp) REVERT: B 220 ASP cc_start: 0.7250 (t70) cc_final: 0.6818 (t0) REVERT: B 344 ARG cc_start: 0.7738 (mpp-170) cc_final: 0.6964 (ttp-110) REVERT: B 383 LYS cc_start: 0.6166 (pttt) cc_final: 0.5839 (ptpt) REVERT: B 389 GLU cc_start: 0.6959 (tp30) cc_final: 0.6532 (mt-10) REVERT: B 444 GLU cc_start: 0.7977 (pm20) cc_final: 0.7411 (mt-10) REVERT: B 477 LEU cc_start: 0.4097 (OUTLIER) cc_final: 0.3763 (tm) REVERT: B 1053 GLU cc_start: 0.6645 (pt0) cc_final: 0.6297 (mt-10) REVERT: B 1132 ARG cc_start: 0.5963 (ttp-170) cc_final: 0.5164 (mtt-85) REVERT: C 193 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7006 (pp20) REVERT: C 197 MET cc_start: 0.6102 (mtm) cc_final: 0.5462 (mtp) REVERT: C 220 ASP cc_start: 0.7267 (t70) cc_final: 0.6853 (t0) REVERT: C 344 ARG cc_start: 0.7752 (mpp-170) cc_final: 0.7094 (ttp-110) REVERT: C 383 LYS cc_start: 0.6135 (pttt) cc_final: 0.5798 (ptpt) REVERT: C 444 GLU cc_start: 0.7976 (pm20) cc_final: 0.7406 (mt-10) REVERT: C 477 LEU cc_start: 0.4090 (OUTLIER) cc_final: 0.3757 (tm) REVERT: C 676 ARG cc_start: 0.7110 (mpp80) cc_final: 0.6479 (mmm-85) REVERT: C 1053 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6485 (mm-30) REVERT: C 1132 ARG cc_start: 0.5953 (ttp-170) cc_final: 0.5167 (mtt-85) REVERT: D 197 MET cc_start: 0.6113 (mtm) cc_final: 0.5628 (mtp) REVERT: D 220 ASP cc_start: 0.7255 (t70) cc_final: 0.6820 (t0) REVERT: D 344 ARG cc_start: 0.7737 (mpp-170) cc_final: 0.7040 (ttp-110) REVERT: D 383 LYS cc_start: 0.6148 (pttt) cc_final: 0.5805 (ptpt) REVERT: D 444 GLU cc_start: 0.7939 (pm20) cc_final: 0.7389 (mt-10) REVERT: D 477 LEU cc_start: 0.4095 (OUTLIER) cc_final: 0.3761 (tm) REVERT: D 676 ARG cc_start: 0.7085 (mpp80) cc_final: 0.6440 (mmm-85) REVERT: D 1053 GLU cc_start: 0.6963 (pt0) cc_final: 0.6629 (mt-10) REVERT: D 1132 ARG cc_start: 0.5940 (ttp-170) cc_final: 0.5150 (mtt-85) outliers start: 58 outliers final: 50 residues processed: 467 average time/residue: 0.5015 time to fit residues: 370.5106 Evaluate side-chains 465 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 409 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1095 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1107 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 371 optimal weight: 0.8980 chunk 391 optimal weight: 0.6980 chunk 357 optimal weight: 0.8980 chunk 380 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 344 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 379 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN ** B 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 GLN ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4960 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35924 Z= 0.162 Angle : 0.471 7.083 48328 Z= 0.240 Chirality : 0.039 0.148 5376 Planarity : 0.004 0.041 5992 Dihedral : 9.677 59.836 6072 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 1.64 % Allowed : 11.53 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.72 (0.13), residues: 4196 helix: 1.71 (0.10), residues: 2556 sheet: -0.60 (0.33), residues: 236 loop : -1.69 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 705 HIS 0.003 0.001 HIS C 250 PHE 0.008 0.001 PHE B 584 TYR 0.012 0.001 TYR C 312 ARG 0.008 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 427 time to evaluate : 3.776 Fit side-chains REVERT: A 197 MET cc_start: 0.6069 (mtm) cc_final: 0.5693 (mtp) REVERT: A 220 ASP cc_start: 0.7319 (t70) cc_final: 0.6900 (t0) REVERT: A 344 ARG cc_start: 0.7780 (mpp-170) cc_final: 0.7062 (ttp-110) REVERT: A 383 LYS cc_start: 0.6258 (pttt) cc_final: 0.5891 (ptpt) REVERT: A 444 GLU cc_start: 0.7972 (pm20) cc_final: 0.7399 (mt-10) REVERT: A 477 LEU cc_start: 0.4064 (OUTLIER) cc_final: 0.3705 (tm) REVERT: A 676 ARG cc_start: 0.7122 (mpp80) cc_final: 0.6494 (mmm-85) REVERT: A 706 MET cc_start: 0.5462 (mmm) cc_final: 0.5127 (mmm) REVERT: A 1053 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6744 (mm-30) REVERT: A 1132 ARG cc_start: 0.5920 (ttp-170) cc_final: 0.5148 (mtt-85) REVERT: B 197 MET cc_start: 0.6069 (mtm) cc_final: 0.5694 (mtp) REVERT: B 220 ASP cc_start: 0.7320 (t70) cc_final: 0.6900 (t0) REVERT: B 344 ARG cc_start: 0.7780 (mpp-170) cc_final: 0.6997 (ttp-110) REVERT: B 383 LYS cc_start: 0.6257 (pttt) cc_final: 0.5887 (ptpt) REVERT: B 389 GLU cc_start: 0.6778 (tp30) cc_final: 0.6349 (mt-10) REVERT: B 403 GLN cc_start: 0.6408 (tt0) cc_final: 0.6143 (tp40) REVERT: B 444 GLU cc_start: 0.7969 (pm20) cc_final: 0.7400 (mt-10) REVERT: B 477 LEU cc_start: 0.4063 (OUTLIER) cc_final: 0.3699 (tm) REVERT: B 1053 GLU cc_start: 0.6584 (pt0) cc_final: 0.6294 (mm-30) REVERT: B 1132 ARG cc_start: 0.5924 (ttp-170) cc_final: 0.5149 (mtt-85) REVERT: C 193 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7174 (pp20) REVERT: C 197 MET cc_start: 0.6043 (mtm) cc_final: 0.5402 (mtp) REVERT: C 220 ASP cc_start: 0.7335 (t70) cc_final: 0.6912 (t0) REVERT: C 344 ARG cc_start: 0.7732 (mpp-170) cc_final: 0.7021 (ttp-110) REVERT: C 383 LYS cc_start: 0.6079 (pttt) cc_final: 0.5721 (ptpt) REVERT: C 444 GLU cc_start: 0.7966 (pm20) cc_final: 0.7398 (mt-10) REVERT: C 477 LEU cc_start: 0.4064 (OUTLIER) cc_final: 0.3702 (tm) REVERT: C 676 ARG cc_start: 0.7067 (mpp80) cc_final: 0.6462 (mmm-85) REVERT: C 706 MET cc_start: 0.5475 (mmm) cc_final: 0.5129 (mmm) REVERT: C 1053 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6524 (mm-30) REVERT: C 1132 ARG cc_start: 0.5936 (ttp-170) cc_final: 0.5148 (mtt-85) REVERT: D 197 MET cc_start: 0.6125 (mtm) cc_final: 0.5635 (mtp) REVERT: D 220 ASP cc_start: 0.7325 (t70) cc_final: 0.6903 (t0) REVERT: D 312 TYR cc_start: 0.6387 (t80) cc_final: 0.6125 (t80) REVERT: D 344 ARG cc_start: 0.7779 (mpp-170) cc_final: 0.7062 (ttp-110) REVERT: D 383 LYS cc_start: 0.6111 (pttt) cc_final: 0.5759 (ptpt) REVERT: D 444 GLU cc_start: 0.7970 (pm20) cc_final: 0.7404 (mt-10) REVERT: D 477 LEU cc_start: 0.4068 (OUTLIER) cc_final: 0.3707 (tm) REVERT: D 676 ARG cc_start: 0.7117 (mpp80) cc_final: 0.6479 (mmm-85) REVERT: D 706 MET cc_start: 0.5469 (mmm) cc_final: 0.5135 (mmm) REVERT: D 1053 GLU cc_start: 0.6895 (pt0) cc_final: 0.6666 (mt-10) REVERT: D 1132 ARG cc_start: 0.5934 (ttp-170) cc_final: 0.5148 (mtt-85) outliers start: 59 outliers final: 48 residues processed: 467 average time/residue: 0.5081 time to fit residues: 374.2562 Evaluate side-chains 468 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 414 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1095 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1095 ASP Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 250 optimal weight: 0.0370 chunk 402 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 422 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 336 optimal weight: 0.0370 chunk 34 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN ** B 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 GLN D 844 ASN ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4958 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35924 Z= 0.159 Angle : 0.471 7.078 48328 Z= 0.240 Chirality : 0.039 0.147 5376 Planarity : 0.004 0.040 5992 Dihedral : 9.554 59.490 6072 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 1.58 % Allowed : 11.53 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.78 (0.13), residues: 4196 helix: 1.74 (0.10), residues: 2560 sheet: -0.54 (0.33), residues: 236 loop : -1.68 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 705 HIS 0.003 0.001 HIS D 250 PHE 0.010 0.001 PHE A 887 TYR 0.018 0.001 TYR D 312 ARG 0.007 0.000 ARG A 480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 420 time to evaluate : 4.429 Fit side-chains REVERT: A 197 MET cc_start: 0.6055 (mtm) cc_final: 0.5676 (mtp) REVERT: A 220 ASP cc_start: 0.7330 (t70) cc_final: 0.6912 (t0) REVERT: A 344 ARG cc_start: 0.7727 (mpp-170) cc_final: 0.6987 (ttp-110) REVERT: A 383 LYS cc_start: 0.6249 (pttt) cc_final: 0.5883 (ptpt) REVERT: A 444 GLU cc_start: 0.7965 (pm20) cc_final: 0.7393 (mt-10) REVERT: A 477 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3718 (tm) REVERT: A 676 ARG cc_start: 0.7125 (mpp80) cc_final: 0.6490 (mmm-85) REVERT: A 706 MET cc_start: 0.5491 (mmm) cc_final: 0.5160 (mmm) REVERT: A 1053 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6961 (mm-30) REVERT: A 1132 ARG cc_start: 0.5920 (ttp-170) cc_final: 0.5148 (mtt-85) REVERT: B 197 MET cc_start: 0.6053 (mtm) cc_final: 0.5675 (mtp) REVERT: B 220 ASP cc_start: 0.7333 (t70) cc_final: 0.6915 (t0) REVERT: B 344 ARG cc_start: 0.7726 (mpp-170) cc_final: 0.6984 (ttp-110) REVERT: B 383 LYS cc_start: 0.6249 (pttt) cc_final: 0.5884 (ptpt) REVERT: B 403 GLN cc_start: 0.6409 (tt0) cc_final: 0.6144 (tp40) REVERT: B 444 GLU cc_start: 0.7977 (pm20) cc_final: 0.7400 (mt-10) REVERT: B 477 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3770 (tm) REVERT: B 676 ARG cc_start: 0.7061 (mpp80) cc_final: 0.6430 (mmm-85) REVERT: B 706 MET cc_start: 0.5502 (mmm) cc_final: 0.5157 (mmm) REVERT: B 1053 GLU cc_start: 0.6611 (pt0) cc_final: 0.6314 (mm-30) REVERT: B 1132 ARG cc_start: 0.5921 (ttp-170) cc_final: 0.5149 (mtt-85) REVERT: C 193 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: C 197 MET cc_start: 0.6018 (mtm) cc_final: 0.5369 (mtp) REVERT: C 220 ASP cc_start: 0.7401 (t70) cc_final: 0.6996 (t0) REVERT: C 344 ARG cc_start: 0.7738 (mpp-170) cc_final: 0.7037 (ttp-110) REVERT: C 383 LYS cc_start: 0.6041 (pttt) cc_final: 0.5674 (ptpt) REVERT: C 444 GLU cc_start: 0.7977 (pm20) cc_final: 0.7397 (mt-10) REVERT: C 477 LEU cc_start: 0.4068 (OUTLIER) cc_final: 0.3706 (tm) REVERT: C 676 ARG cc_start: 0.7065 (mpp80) cc_final: 0.6464 (mmm-85) REVERT: C 706 MET cc_start: 0.5496 (mmm) cc_final: 0.5165 (mmm) REVERT: C 1053 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6512 (mm-30) REVERT: C 1132 ARG cc_start: 0.5934 (ttp-170) cc_final: 0.5149 (mtt-85) REVERT: D 197 MET cc_start: 0.6054 (mtm) cc_final: 0.5684 (mtp) REVERT: D 220 ASP cc_start: 0.7333 (t70) cc_final: 0.6912 (t0) REVERT: D 312 TYR cc_start: 0.6385 (t80) cc_final: 0.5799 (t80) REVERT: D 344 ARG cc_start: 0.7728 (mpp-170) cc_final: 0.6988 (ttp-110) REVERT: D 383 LYS cc_start: 0.6105 (pttt) cc_final: 0.5765 (ptpt) REVERT: D 444 GLU cc_start: 0.7977 (pm20) cc_final: 0.7402 (mt-10) REVERT: D 477 LEU cc_start: 0.4077 (OUTLIER) cc_final: 0.3715 (tm) REVERT: D 676 ARG cc_start: 0.7108 (mpp80) cc_final: 0.6473 (mmm-85) REVERT: D 706 MET cc_start: 0.5476 (mmm) cc_final: 0.5145 (mmm) REVERT: D 1053 GLU cc_start: 0.6840 (pt0) cc_final: 0.6517 (mm-30) REVERT: D 1132 ARG cc_start: 0.5931 (ttp-170) cc_final: 0.5148 (mtt-85) outliers start: 57 outliers final: 45 residues processed: 457 average time/residue: 0.5205 time to fit residues: 376.5165 Evaluate side-chains 464 residues out of total 3708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 413 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASN Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1107 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 1061 LEU Chi-restraints excluded: chain B residue 1071 VAL Chi-restraints excluded: chain B residue 1095 ASP Chi-restraints excluded: chain B residue 1107 LEU Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1071 VAL Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 574 ASP Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 1061 LEU Chi-restraints excluded: chain D residue 1071 VAL Chi-restraints excluded: chain D residue 1095 ASP Chi-restraints excluded: chain D residue 1107 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 267 optimal weight: 5.9990 chunk 358 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 310 optimal weight: 0.0170 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 336 optimal weight: 0.0570 chunk 140 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 42 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 844 ASN B 983 GLN C 983 GLN D 844 ASN ** D 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105075 restraints weight = 43489.935| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.91 r_work: 0.2962 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35924 Z= 0.143 Angle : 0.458 7.038 48328 Z= 0.234 Chirality : 0.038 0.147 5376 Planarity : 0.004 0.045 5992 Dihedral : 9.225 59.350 6072 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 1.47 % Allowed : 11.67 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.13), residues: 4196 helix: 1.85 (0.10), residues: 2560 sheet: -0.47 (0.33), residues: 236 loop : -1.60 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 705 HIS 0.002 0.001 HIS A 250 PHE 0.011 0.001 PHE A 887 TYR 0.011 0.001 TYR D 338 ARG 0.009 0.000 ARG A 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8694.66 seconds wall clock time: 157 minutes 13.76 seconds (9433.76 seconds total)