Starting phenix.real_space_refine on Fri Feb 23 12:31:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oky_12973/02_2024/7oky_12973.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oky_12973/02_2024/7oky_12973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oky_12973/02_2024/7oky_12973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oky_12973/02_2024/7oky_12973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oky_12973/02_2024/7oky_12973.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oky_12973/02_2024/7oky_12973.pdb" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.990 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 Zn 9 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 230 5.16 5 C 23946 2.51 5 N 6740 2.21 5 O 7336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 448": "NH1" <-> "NH2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A GLU 762": "OE1" <-> "OE2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A ARG 1059": "NH1" <-> "NH2" Residue "A GLU 1063": "OE1" <-> "OE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1349": "OE1" <-> "OE2" Residue "A GLU 1364": "OE1" <-> "OE2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "A GLU 1478": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 593": "OE1" <-> "OE2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B GLU 893": "OE1" <-> "OE2" Residue "B GLU 895": "OE1" <-> "OE2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B GLU 904": "OE1" <-> "OE2" Residue "B GLU 907": "OE1" <-> "OE2" Residue "B GLU 977": "OE1" <-> "OE2" Residue "B GLU 1029": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1153": "OE1" <-> "OE2" Residue "B PHE 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1208": "NH1" <-> "NH2" Residue "B GLU 1238": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M GLU 12": "OE1" <-> "OE2" Residue "M GLU 36": "OE1" <-> "OE2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 135": "NH1" <-> "NH2" Residue "O TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 49": "OE1" <-> "OE2" Residue "O GLU 57": "OE1" <-> "OE2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z GLU 259": "OE1" <-> "OE2" Residue "Z GLU 523": "OE1" <-> "OE2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ARG 582": "NH1" <-> "NH2" Residue "Z GLU 590": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38341 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1407, 11149 Classifications: {'peptide': 1407} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1338} Chain breaks: 6 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 9047 Classifications: {'peptide': 1131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1077} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1347 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 932 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1106 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "O" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 832 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 279 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Chain: "T" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "Z" Number of atoms: 2979 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 2971 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 374, 2971 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 3011 Chain: "Y" Number of atoms: 920 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 899 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 107.327 100.777 77.923 1.00 53.97 S ATOM 494 SG CYS A 74 106.063 104.031 79.616 1.00 50.43 S ATOM 541 SG CYS A 81 103.720 101.015 79.304 1.00 45.79 S ATOM 776 SG CYS A 111 89.795 108.014 34.549 1.00 65.63 S ATOM 804 SG CYS A 114 91.516 111.137 34.607 1.00 69.86 S ATOM 1117 SG CYS A 154 87.909 110.902 33.075 1.00 76.79 S ATOM 1144 SG CYS A 184 91.027 109.611 31.192 1.00 79.71 S ATOM 19765 SG CYS B1196 100.691 116.592 70.371 1.00 45.35 S ATOM 19787 SG CYS B1199 99.408 113.716 68.144 1.00 49.68 S ATOM 19902 SG CYS B1214 102.643 113.412 69.466 1.00 52.69 S ATOM 19923 SG CYS B1217 101.947 116.115 66.748 1.00 64.76 S ATOM 20890 SG CYS C 88 82.640 78.966 138.530 1.00 49.61 S ATOM 20903 SG CYS C 90 85.274 77.668 136.016 1.00 55.35 S ATOM 20938 SG CYS C 94 84.071 75.646 138.950 1.00 41.65 S ATOM 20960 SG CYS C 97 81.805 76.249 135.891 1.00 37.01 S ATOM 28729 SG CYS I 86 20.547 53.417 55.946 1.00 62.37 S ATOM 28753 SG CYS I 89 20.323 49.626 56.631 1.00 69.05 S ATOM 28957 SG CYS I 114 23.091 51.800 58.188 1.00 51.27 S ATOM 28992 SG CYS I 119 22.954 50.881 54.427 1.00 64.00 S ATOM 28177 SG CYS I 17 49.191 59.227 21.712 1.00 35.13 S ATOM 28201 SG CYS I 20 53.027 60.186 22.885 1.00 34.24 S ATOM 28352 SG CYS I 39 50.448 62.435 22.195 1.00 45.53 S ATOM 28377 SG CYS I 42 51.765 59.890 19.133 1.00 49.82 S ATOM 29102 SG CYS J 7 57.094 68.010 118.927 1.00 15.25 S ATOM 29126 SG CYS J 10 56.162 69.229 122.392 1.00 15.23 S ATOM 29390 SG CYS J 44 53.495 69.170 119.515 1.00 20.26 S ATOM 29396 SG CYS J 45 54.680 66.166 121.444 1.00 21.78 S ATOM 30533 SG CYS L 19 92.862 49.429 101.464 1.00 49.50 S ATOM 30552 SG CYS L 22 93.230 46.562 103.807 1.00 53.06 S ATOM 30663 SG CYS L 36 96.223 47.633 101.965 1.00 57.01 S ATOM 30689 SG CYS L 39 93.449 45.922 100.005 1.00 56.16 S ATOM 37530 SG CYS Y 16 127.725 65.380 30.388 1.00 13.45 S ATOM 37552 SG CYS Y 19 124.571 64.597 28.442 1.00 12.79 S ATOM 37664 SG CYS Y 33 126.661 61.860 29.266 1.00 14.97 S ATOM 37686 SG CYS Y 36 127.942 64.265 26.644 1.00 15.83 S Time building chain proxies: 21.25, per 1000 atoms: 0.55 Number of scatterers: 38341 At special positions: 0 Unit cell: (159.6, 172.2, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 9 29.99 S 230 16.00 P 79 15.00 Mg 1 11.99 O 7336 8.00 N 6740 7.00 C 23946 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 Time building additional restraints: 14.52 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1199 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1214 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1196 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1217 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " Number of angles added : 51 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8640 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 57 sheets defined 34.9% alpha, 20.4% beta 27 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 12.94 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.683A pdb=" N GLY A 63 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.594A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.600A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.571A pdb=" N ASN A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.579A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.503A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.520A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.581A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.708A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.704A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.510A pdb=" N ARG A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 934 removed outlier: 4.222A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.728A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1102 removed outlier: 3.537A pdb=" N MET A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.594A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1162 Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1223 removed outlier: 3.644A pdb=" N ASP A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1294 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.670A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.504A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.900A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.636A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.843A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1479 through 1483 removed outlier: 3.837A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1479 through 1483' Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.857A pdb=" N TRP B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.804A pdb=" N SER B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 244 through 251 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 371 through 378 removed outlier: 4.087A pdb=" N MET B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 385 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.592A pdb=" N VAL B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 502 removed outlier: 3.769A pdb=" N GLY B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 501 " --> pdb=" O GLN B 497 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.514A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 520 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.792A pdb=" N GLU B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 633 No H-bonds generated for 'chain 'B' and resid 631 through 633' Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.855A pdb=" N ILE B 638 " --> pdb=" O PRO B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.512A pdb=" N ILE B 717 " --> pdb=" O LYS B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 removed outlier: 3.640A pdb=" N ASN B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 744 through 748 removed outlier: 3.588A pdb=" N GLU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 748' Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 776 through 781 removed outlier: 3.757A pdb=" N ILE B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 removed outlier: 3.580A pdb=" N ASN B 794 " --> pdb=" O PRO B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 838 through 843 removed outlier: 3.754A pdb=" N GLU B 842 " --> pdb=" O ARG B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 875 through 880 Processing helix chain 'B' and resid 921 through 925 removed outlier: 4.004A pdb=" N LYS B 924 " --> pdb=" O ILE B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.911A pdb=" N LEU B1058 " --> pdb=" O THR B1054 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1094 Processing helix chain 'B' and resid 1154 through 1158 removed outlier: 3.623A pdb=" N ARG B1157 " --> pdb=" O GLY B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1229 through 1241 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.568A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 removed outlier: 3.594A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 84 through 92 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.879A pdb=" N LYS D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 158 through 161 removed outlier: 3.523A pdb=" N GLU D 161 " --> pdb=" O PRO D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 161' Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.554A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.698A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.643A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.591A pdb=" N GLU G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.690A pdb=" N ASP H 86 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.573A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.754A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.000A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 35 through 48 removed outlier: 3.601A pdb=" N HIS M 48 " --> pdb=" O THR M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 146 removed outlier: 3.900A pdb=" N GLN M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 23 removed outlier: 3.543A pdb=" N PHE O 22 " --> pdb=" O GLY O 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 204 removed outlier: 4.081A pdb=" N ALA Z 193 " --> pdb=" O GLU Z 189 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE Z 194 " --> pdb=" O ARG Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 231 through 239 Processing helix chain 'Z' and resid 242 through 246 removed outlier: 3.581A pdb=" N LEU Z 245 " --> pdb=" O VAL Z 242 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG Z 246 " --> pdb=" O GLY Z 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 242 through 246' Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.845A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.764A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 4.041A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR Y 50 " --> pdb=" O ARG Y 46 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 75 removed outlier: 3.783A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 104 removed outlier: 3.626A pdb=" N AARG Y 104 " --> pdb=" O GLU Y 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.704A pdb=" N ARG A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.772A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.586A pdb=" N GLU A 201 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.585A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 5.914A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.587A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.347A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.656A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 3.936A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1164 through 1165 removed outlier: 6.897A pdb=" N THR A1164 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1243 through 1248 removed outlier: 4.117A pdb=" N ASN A1248 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A1256 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N ALA A1171 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS I 57 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR A1173 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL I 55 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A1175 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB9, first strand: chain 'A' and resid 1408 through 1409 removed outlier: 4.121A pdb=" N GLN E 174 " --> pdb=" O GLY A1409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 72 through 73 removed outlier: 4.479A pdb=" N GLU D 72 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.108A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN G 53 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS G 71 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE G 51 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS G 73 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 47 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE G 77 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 142 through 144 removed outlier: 4.489A pdb=" N ASP B 204 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 202 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 170 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 199 " --> pdb=" O GLY B 227 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY B 227 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU B 201 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE B 225 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL B 203 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC5, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC6, first strand: chain 'B' and resid 468 through 471 removed outlier: 6.414A pdb=" N ALA B 273 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 282 through 285 removed outlier: 3.650A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP B 313 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AC9, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD1, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.494A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.103A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B1003 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR B 978 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.103A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE B 995 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 986 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 997 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 984 " --> pdb=" O LYS B 997 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG B 999 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B1003 " --> pdb=" O THR B 978 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR B 978 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.081A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 897 through 898 removed outlier: 4.942A pdb=" N GLU B 903 " --> pdb=" O THR B 949 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 949 " --> pdb=" O GLU B 903 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN B 915 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 942 through 944 removed outlier: 7.414A pdb=" N THR B 971 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1192 through 1196 Processing sheet with id=AD9, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AE1, first strand: chain 'C' and resid 8 through 15 removed outlier: 5.838A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 18 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG C 228 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR C 186 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.986A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.048A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 92 removed outlier: 3.730A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF2, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.471A pdb=" N ARG O 17 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 112 through 117 removed outlier: 6.965A pdb=" N CYS M 99 " --> pdb=" O LEU M 115 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE M 117 " --> pdb=" O PHE M 97 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE M 97 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE O 33 " --> pdb=" O ASP M 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE O 30 " --> pdb=" O SER O 104 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ILE O 106 " --> pdb=" O PHE O 30 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR O 32 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL O 108 " --> pdb=" O THR O 32 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG O 34 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS O 110 " --> pdb=" O ARG O 34 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP O 36 " --> pdb=" O LYS O 110 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL O 74 " --> pdb=" O THR O 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 253 through 254 removed outlier: 3.542A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL Z 215 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA Z 217 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 267 through 268 removed outlier: 3.500A pdb=" N LYS Z 268 " --> pdb=" O ILE Y 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'Z' and resid 510 through 513 removed outlier: 7.180A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.175A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 586 through 587 removed outlier: 3.519A pdb=" N ALA Z 586 " --> pdb=" O ILE Z 594 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 635 through 639 removed outlier: 7.274A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.691A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 22 through 24 1474 hydrogen bonds defined for protein. 4076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 21.30 Time building geometry restraints manager: 15.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6330 1.32 - 1.44: 10241 1.44 - 1.57: 22126 1.57 - 1.69: 156 1.69 - 1.82: 360 Bond restraints: 39213 Sorted by residual: bond pdb=" C PRO J 64 " pdb=" O PRO J 64 " ideal model delta sigma weight residual 1.234 1.192 0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" CG LEU B 480 " pdb=" CD1 LEU B 480 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.85e+00 bond pdb=" N VAL A 538 " pdb=" CA VAL A 538 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.15e-02 7.56e+03 6.00e+00 bond pdb=" C GLN A 539 " pdb=" O GLN A 539 " ideal model delta sigma weight residual 1.241 1.214 0.026 1.08e-02 8.57e+03 5.88e+00 bond pdb=" N LEU J 65 " pdb=" CA LEU J 65 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.21e-02 6.83e+03 5.13e+00 ... (remaining 39208 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.46: 640 103.46 - 111.13: 15104 111.13 - 118.80: 16683 118.80 - 126.46: 20159 126.46 - 134.13: 710 Bond angle restraints: 53296 Sorted by residual: angle pdb=" C AARG Y 104 " pdb=" N GLY Y 105 " pdb=" CA GLY Y 105 " ideal model delta sigma weight residual 121.70 131.22 -9.52 1.80e+00 3.09e-01 2.80e+01 angle pdb=" C CYS I 20 " pdb=" N ASN I 21 " pdb=" CA ASN I 21 " ideal model delta sigma weight residual 122.74 130.25 -7.51 1.44e+00 4.82e-01 2.72e+01 angle pdb=" N GLN A 539 " pdb=" CA GLN A 539 " pdb=" C GLN A 539 " ideal model delta sigma weight residual 108.00 114.86 -6.86 1.48e+00 4.57e-01 2.15e+01 angle pdb=" CB MET Z 451 " pdb=" CG MET Z 451 " pdb=" SD MET Z 451 " ideal model delta sigma weight residual 112.70 126.58 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C GLY A 536 " pdb=" N ILE A 537 " pdb=" CA ILE A 537 " ideal model delta sigma weight residual 121.80 115.75 6.05 1.40e+00 5.10e-01 1.87e+01 ... (remaining 53291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 23074 34.96 - 69.92: 711 69.92 - 104.88: 70 104.88 - 139.84: 0 139.84 - 174.80: 1 Dihedral angle restraints: 23856 sinusoidal: 10497 harmonic: 13359 Sorted by residual: dihedral pdb=" CA ASN G 124 " pdb=" C ASN G 124 " pdb=" N PRO G 125 " pdb=" CA PRO G 125 " ideal model delta harmonic sigma weight residual 180.00 140.82 39.18 0 5.00e+00 4.00e-02 6.14e+01 dihedral pdb=" CA MET G 117 " pdb=" C MET G 117 " pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta harmonic sigma weight residual 180.00 -148.92 -31.08 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASN G 122 " pdb=" C ASN G 122 " pdb=" N SER G 123 " pdb=" CA SER G 123 " ideal model delta harmonic sigma weight residual 180.00 150.11 29.89 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 23853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 5619 0.102 - 0.204: 342 0.204 - 0.306: 9 0.306 - 0.408: 2 0.408 - 0.510: 3 Chirality restraints: 5975 Sorted by residual: chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" CB VAL Y 6 " pdb=" CA VAL Y 6 " pdb=" CG1 VAL Y 6 " pdb=" CG2 VAL Y 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CG LEU A 831 " pdb=" CB LEU A 831 " pdb=" CD1 LEU A 831 " pdb=" CD2 LEU A 831 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 5972 not shown) Planarity restraints: 6626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Y 93 " 0.102 5.00e-02 4.00e+02 1.53e-01 3.74e+01 pdb=" N PRO Y 94 " -0.264 5.00e-02 4.00e+02 pdb=" CA PRO Y 94 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO Y 94 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 536 " 0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C GLY A 536 " -0.065 2.00e-02 2.50e+03 pdb=" O GLY A 536 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE A 537 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 829 " -0.025 2.00e-02 2.50e+03 2.13e-02 9.09e+00 pdb=" CG TYR B 829 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 829 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 829 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 829 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 829 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 829 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 829 " -0.002 2.00e-02 2.50e+03 ... (remaining 6623 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 577 2.65 - 3.22: 33004 3.22 - 3.78: 62040 3.78 - 4.34: 88434 4.34 - 4.90: 141885 Nonbonded interactions: 325940 Sorted by model distance: nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.093 2.170 nonbonded pdb=" ND1 HIS O 31 " pdb=" OG SER O 104 " model vdw 2.097 2.520 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.106 2.170 nonbonded pdb=" O3' A P 46 " pdb="MG MG A2001 " model vdw 2.107 2.170 nonbonded pdb=" OG SER B 938 " pdb=" OE2 GLU Z 735 " model vdw 2.123 2.440 ... (remaining 325935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.100 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 119.490 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 : 0.004 0.092 39213 Z= 0.292 Angle : 0.758 13.877 53296 Z= 0.423 Chirality : 0.051 0.510 5975 Planarity : 0.006 0.153 6626 Dihedral : 16.233 174.796 15216 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.02 % Allowed : 0.47 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4537 helix: -0.84 (0.12), residues: 1411 sheet: -1.02 (0.18), residues: 770 loop : -0.72 (0.12), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 530 HIS 0.013 0.001 HIS B 464 PHE 0.050 0.002 PHE A 112 TYR 0.052 0.002 TYR B 829 ARG 0.029 0.001 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 652 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7302 (mtm) cc_final: 0.6809 (mtt) REVERT: A 339 LEU cc_start: 0.9021 (mt) cc_final: 0.8629 (mt) REVERT: A 355 MET cc_start: 0.8098 (mmm) cc_final: 0.7828 (mmp) REVERT: A 524 MET cc_start: 0.8183 (mmp) cc_final: 0.7898 (mmm) REVERT: A 1097 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 1484 MET cc_start: 0.6149 (ptp) cc_final: 0.5583 (ptm) REVERT: B 206 THR cc_start: 0.6202 (p) cc_final: 0.5641 (p) REVERT: B 377 MET cc_start: 0.8334 (mtp) cc_final: 0.7696 (mtp) REVERT: B 653 ILE cc_start: 0.8969 (pt) cc_final: 0.8445 (pt) REVERT: D 174 ASP cc_start: 0.7018 (m-30) cc_final: 0.6730 (t70) REVERT: F 84 GLU cc_start: 0.7478 (mp0) cc_final: 0.6648 (mp0) REVERT: F 98 LYS cc_start: 0.8370 (mttt) cc_final: 0.8070 (mtpp) REVERT: F 125 ILE cc_start: 0.8828 (mm) cc_final: 0.8571 (mp) REVERT: H 9 ILE cc_start: 0.8962 (mm) cc_final: 0.8736 (pt) REVERT: H 37 MET cc_start: 0.7955 (mmt) cc_final: 0.7302 (mmt) REVERT: I 68 ILE cc_start: 0.8820 (mt) cc_final: 0.8095 (mt) REVERT: I 98 GLN cc_start: 0.7955 (mt0) cc_final: 0.7744 (mt0) REVERT: I 110 LEU cc_start: 0.8846 (mt) cc_final: 0.8477 (mt) REVERT: J 58 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8741 (mmtt) REVERT: K 25 THR cc_start: 0.7963 (p) cc_final: 0.7561 (t) REVERT: L 15 MET cc_start: 0.6769 (tpp) cc_final: 0.6354 (tpp) REVERT: M 80 ASN cc_start: 0.6131 (m-40) cc_final: 0.5847 (m-40) REVERT: M 133 MET cc_start: 0.7459 (ppp) cc_final: 0.5814 (ppp) REVERT: O 16 LEU cc_start: 0.5258 (tt) cc_final: 0.4703 (tt) REVERT: Z 254 MET cc_start: 0.5229 (tpt) cc_final: 0.5014 (tpt) REVERT: Z 460 MET cc_start: 0.4667 (tmm) cc_final: 0.4247 (tpp) REVERT: Z 474 MET cc_start: -0.1960 (mmp) cc_final: -0.2332 (mmp) REVERT: Z 481 ILE cc_start: 0.5446 (mt) cc_final: 0.5096 (mt) outliers start: 1 outliers final: 1 residues processed: 652 average time/residue: 0.5916 time to fit residues: 597.8089 Evaluate side-chains 328 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 327 time to evaluate : 5.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 20.0000 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 414 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 671 ASN A 735 GLN A1244 ASN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 GLN B 188 ASN B 537 HIS ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 ASN B1171 GLN C 5 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN D 90 ASN D 131 GLN H 133 HIS I 18 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN M 140 GLN Z 232 GLN ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 39213 Z= 0.252 Angle : 0.581 10.055 53296 Z= 0.307 Chirality : 0.044 0.258 5975 Planarity : 0.005 0.098 6626 Dihedral : 12.636 173.675 5942 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.12 % Allowed : 3.34 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: -0.47 (0.12), residues: 4537 helix: 0.29 (0.14), residues: 1434 sheet: -0.75 (0.18), residues: 771 loop : -0.43 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 583 HIS 0.006 0.001 HIS A 809 PHE 0.029 0.001 PHE A 458 TYR 0.035 0.001 TYR B 465 ARG 0.007 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 412 time to evaluate : 5.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8382 (mtm) cc_final: 0.7912 (mpp) REVERT: A 329 MET cc_start: 0.7741 (mtm) cc_final: 0.7417 (mtm) REVERT: A 520 MET cc_start: 0.8263 (mmm) cc_final: 0.8057 (mmt) REVERT: A 565 MET cc_start: 0.8509 (mmm) cc_final: 0.7669 (mmm) REVERT: A 652 LEU cc_start: 0.9151 (tp) cc_final: 0.8941 (tt) REVERT: A 1097 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 1484 MET cc_start: 0.5995 (ptp) cc_final: 0.5656 (ptm) REVERT: B 606 MET cc_start: 0.9038 (mmm) cc_final: 0.8676 (mpp) REVERT: F 97 LEU cc_start: 0.9077 (tp) cc_final: 0.8852 (tt) REVERT: F 98 LYS cc_start: 0.8335 (mttt) cc_final: 0.8126 (mtpp) REVERT: I 46 GLN cc_start: 0.6492 (pp30) cc_final: 0.6114 (pp30) REVERT: I 57 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7951 (mmtt) REVERT: I 68 ILE cc_start: 0.8777 (mt) cc_final: 0.8083 (mt) REVERT: I 98 GLN cc_start: 0.6575 (tt0) cc_final: 0.6149 (mt0) REVERT: I 108 MET cc_start: 0.8160 (mmt) cc_final: 0.7188 (mmp) REVERT: K 13 PHE cc_start: 0.8015 (p90) cc_final: 0.6818 (p90) REVERT: K 25 THR cc_start: 0.7982 (p) cc_final: 0.7644 (t) REVERT: K 93 ASP cc_start: 0.7624 (m-30) cc_final: 0.7411 (m-30) REVERT: L 52 LEU cc_start: 0.9521 (tt) cc_final: 0.9320 (tt) REVERT: M 80 ASN cc_start: 0.6352 (m-40) cc_final: 0.6051 (m-40) REVERT: M 133 MET cc_start: 0.6848 (ppp) cc_final: 0.6254 (ppp) REVERT: M 138 MET cc_start: 0.4631 (mmt) cc_final: 0.4271 (ttm) REVERT: O 35 TYR cc_start: 0.6717 (m-80) cc_final: 0.6507 (m-10) REVERT: O 36 ASP cc_start: 0.7197 (p0) cc_final: 0.6672 (p0) REVERT: Z 460 MET cc_start: 0.4601 (tmm) cc_final: 0.4010 (tpp) REVERT: Z 474 MET cc_start: -0.1659 (mmp) cc_final: -0.2558 (mmp) REVERT: Z 481 ILE cc_start: 0.5501 (mt) cc_final: 0.5156 (mt) outliers start: 5 outliers final: 0 residues processed: 417 average time/residue: 0.5436 time to fit residues: 362.9584 Evaluate side-chains 291 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 344 optimal weight: 8.9990 chunk 281 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 414 optimal weight: 0.0670 chunk 448 optimal weight: 0.0470 chunk 369 optimal weight: 6.9990 chunk 411 optimal weight: 40.0000 chunk 141 optimal weight: 4.9990 chunk 332 optimal weight: 40.0000 overall best weight: 3.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 273 GLN A 377 GLN A1384 HIS B 188 ASN B 537 HIS B 595 HIS B 602 ASN B1171 GLN C 32 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 GLN O 107 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 232 GLN ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 39213 Z= 0.316 Angle : 0.588 15.160 53296 Z= 0.307 Chirality : 0.044 0.212 5975 Planarity : 0.004 0.092 6626 Dihedral : 12.574 175.174 5942 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: -0.08 (0.12), residues: 4537 helix: 0.78 (0.14), residues: 1436 sheet: -0.69 (0.18), residues: 773 loop : -0.24 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.011 0.001 HIS A 204 PHE 0.023 0.001 PHE I 11 TYR 0.024 0.002 TYR B 465 ARG 0.007 0.001 ARG M 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 374 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.7936 (mtm) cc_final: 0.7736 (mtm) REVERT: A 565 MET cc_start: 0.8531 (mmm) cc_final: 0.7730 (mmm) REVERT: A 1097 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 1484 MET cc_start: 0.6127 (ptp) cc_final: 0.5631 (ptm) REVERT: E 151 MET cc_start: 0.8228 (mtp) cc_final: 0.7957 (mtp) REVERT: F 97 LEU cc_start: 0.9108 (tp) cc_final: 0.8887 (tt) REVERT: F 125 ILE cc_start: 0.8951 (mm) cc_final: 0.8737 (mm) REVERT: G 29 LYS cc_start: 0.7785 (mttm) cc_final: 0.6993 (mmmm) REVERT: H 76 ASN cc_start: 0.8537 (t0) cc_final: 0.8322 (m-40) REVERT: I 46 GLN cc_start: 0.6586 (pp30) cc_final: 0.6087 (pp30) REVERT: I 108 MET cc_start: 0.8195 (mmt) cc_final: 0.7826 (mmm) REVERT: K 25 THR cc_start: 0.7951 (p) cc_final: 0.7648 (t) REVERT: M 138 MET cc_start: 0.4824 (mmt) cc_final: 0.4456 (ttt) REVERT: O 109 LYS cc_start: 0.6549 (mtpp) cc_final: 0.6226 (mtpp) REVERT: Z 460 MET cc_start: 0.4467 (tmm) cc_final: 0.3887 (tpp) REVERT: Z 481 ILE cc_start: 0.5263 (mt) cc_final: 0.4904 (mt) REVERT: Y 64 MET cc_start: 0.4093 (pmm) cc_final: 0.3515 (pmm) outliers start: 4 outliers final: 1 residues processed: 376 average time/residue: 0.5512 time to fit residues: 332.8206 Evaluate side-chains 268 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 4.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 5.9990 chunk 311 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 278 optimal weight: 0.0070 chunk 416 optimal weight: 20.0000 chunk 440 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 394 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 595 HIS B 919 HIS ** B1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 260 GLN D 61 GLN D 171 GLN G 53 ASN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 29 ASN M 140 GLN O 107 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 232 GLN ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39213 Z= 0.187 Angle : 0.526 10.691 53296 Z= 0.276 Chirality : 0.043 0.197 5975 Planarity : 0.004 0.096 6626 Dihedral : 12.474 177.724 5942 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.07 % Allowed : 2.04 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.11 (0.13), residues: 4537 helix: 0.95 (0.14), residues: 1445 sheet: -0.51 (0.18), residues: 759 loop : -0.19 (0.13), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.006 0.001 HIS G 4 PHE 0.025 0.001 PHE A 458 TYR 0.021 0.001 TYR M 84 ARG 0.008 0.000 ARG A 928 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 347 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8532 (mmm) cc_final: 0.7793 (mmm) REVERT: A 1097 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 1484 MET cc_start: 0.6040 (ptp) cc_final: 0.5497 (ptm) REVERT: B 868 GLU cc_start: 0.7216 (tp30) cc_final: 0.6499 (tp30) REVERT: E 151 MET cc_start: 0.8184 (mtp) cc_final: 0.7931 (mtp) REVERT: I 46 GLN cc_start: 0.6482 (pp30) cc_final: 0.6146 (pp30) REVERT: I 108 MET cc_start: 0.8177 (mmt) cc_final: 0.7671 (mmp) REVERT: K 25 THR cc_start: 0.7975 (p) cc_final: 0.7695 (t) REVERT: Z 460 MET cc_start: 0.4340 (tmm) cc_final: 0.3806 (tpp) REVERT: Z 474 MET cc_start: -0.2051 (mmp) cc_final: -0.2641 (mmp) REVERT: Z 481 ILE cc_start: 0.5255 (mt) cc_final: 0.4866 (mt) REVERT: Y 64 MET cc_start: 0.3905 (pmm) cc_final: 0.3473 (pmm) outliers start: 3 outliers final: 0 residues processed: 348 average time/residue: 0.5450 time to fit residues: 306.5027 Evaluate side-chains 264 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 4.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 328 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 376 optimal weight: 7.9990 chunk 304 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 395 optimal weight: 0.0970 chunk 111 optimal weight: 7.9990 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN B 188 ASN B 595 HIS D 171 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 89 ASN M 48 HIS O 92 HIS O 107 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39213 Z= 0.323 Angle : 0.565 11.425 53296 Z= 0.295 Chirality : 0.044 0.256 5975 Planarity : 0.004 0.097 6626 Dihedral : 12.466 179.374 5942 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.07 % Allowed : 1.62 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.17 (0.13), residues: 4537 helix: 1.01 (0.14), residues: 1452 sheet: -0.49 (0.18), residues: 763 loop : -0.15 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.005 0.001 HIS Y 12 PHE 0.016 0.001 PHE A 592 TYR 0.047 0.001 TYR B1125 ARG 0.005 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 329 time to evaluate : 4.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 MET cc_start: 0.8557 (mmm) cc_final: 0.7799 (mmm) REVERT: A 1484 MET cc_start: 0.6229 (ptp) cc_final: 0.5683 (ptm) REVERT: E 151 MET cc_start: 0.8305 (mtp) cc_final: 0.8073 (mtp) REVERT: G 29 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7416 (mmmm) REVERT: I 46 GLN cc_start: 0.6660 (pp30) cc_final: 0.6306 (pp30) REVERT: I 69 ILE cc_start: 0.9055 (pt) cc_final: 0.8807 (mp) REVERT: Z 460 MET cc_start: 0.4465 (tmm) cc_final: 0.3989 (tpp) REVERT: Z 474 MET cc_start: -0.1788 (mmp) cc_final: -0.2408 (mmp) REVERT: Z 481 ILE cc_start: 0.5224 (mt) cc_final: 0.4823 (mt) REVERT: Y 37 ASP cc_start: 0.1183 (m-30) cc_final: 0.0658 (m-30) REVERT: Y 64 MET cc_start: 0.4375 (pmm) cc_final: 0.4010 (pmm) outliers start: 3 outliers final: 1 residues processed: 329 average time/residue: 0.5835 time to fit residues: 311.1775 Evaluate side-chains 257 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 0.9990 chunk 396 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 441 optimal weight: 7.9990 chunk 366 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 145 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 GLN B 188 ASN B 919 HIS C 6 GLN C 32 ASN D 61 GLN D 171 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN O 107 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39213 Z= 0.172 Angle : 0.511 9.745 53296 Z= 0.267 Chirality : 0.043 0.209 5975 Planarity : 0.004 0.101 6626 Dihedral : 12.415 179.137 5942 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.05 % Allowed : 1.33 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.31 (0.13), residues: 4537 helix: 1.17 (0.14), residues: 1449 sheet: -0.39 (0.18), residues: 770 loop : -0.10 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.005 0.001 HIS K 69 PHE 0.019 0.001 PHE A 458 TYR 0.017 0.001 TYR O 97 ARG 0.004 0.000 ARG D 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 338 time to evaluate : 5.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8617 (tpp) cc_final: 0.8307 (tpp) REVERT: A 310 LEU cc_start: 0.8969 (tp) cc_final: 0.8758 (tp) REVERT: A 565 MET cc_start: 0.8533 (mmm) cc_final: 0.7811 (mmm) REVERT: A 1097 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 1484 MET cc_start: 0.5966 (ptp) cc_final: 0.5410 (ptm) REVERT: E 151 MET cc_start: 0.8252 (mtp) cc_final: 0.8008 (mtp) REVERT: G 29 LYS cc_start: 0.7822 (mmtp) cc_final: 0.7302 (mmmm) REVERT: G 37 THR cc_start: 0.7058 (p) cc_final: 0.6857 (p) REVERT: G 53 ASN cc_start: 0.5592 (p0) cc_final: 0.5341 (p0) REVERT: I 46 GLN cc_start: 0.6476 (pp30) cc_final: 0.6160 (pp30) REVERT: I 69 ILE cc_start: 0.9060 (pt) cc_final: 0.8836 (mp) REVERT: I 108 MET cc_start: 0.8538 (mmm) cc_final: 0.7769 (mmm) REVERT: O 36 ASP cc_start: 0.6983 (p0) cc_final: 0.6732 (p0) REVERT: Z 460 MET cc_start: 0.4403 (tmm) cc_final: 0.3923 (tpp) REVERT: Z 474 MET cc_start: -0.1915 (mmp) cc_final: -0.2395 (mmp) REVERT: Z 481 ILE cc_start: 0.5202 (mt) cc_final: 0.4809 (mt) REVERT: Y 37 ASP cc_start: 0.1302 (m-30) cc_final: 0.0748 (m-30) REVERT: Y 64 MET cc_start: 0.4414 (pmm) cc_final: 0.4089 (pmm) outliers start: 2 outliers final: 0 residues processed: 338 average time/residue: 0.5423 time to fit residues: 297.0307 Evaluate side-chains 255 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 251 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 439 optimal weight: 50.0000 chunk 275 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS A1313 GLN B 188 ASN ** B 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN D 171 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 GLN O 107 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 573 GLN ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 39213 Z= 0.215 Angle : 0.527 10.094 53296 Z= 0.273 Chirality : 0.043 0.188 5975 Planarity : 0.004 0.096 6626 Dihedral : 12.375 178.075 5942 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.05 % Allowed : 0.98 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.37 (0.13), residues: 4537 helix: 1.25 (0.14), residues: 1444 sheet: -0.34 (0.18), residues: 773 loop : -0.09 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.013 0.001 HIS I 100 PHE 0.015 0.001 PHE B 882 TYR 0.023 0.001 TYR B1125 ARG 0.011 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 324 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8566 (tpp) cc_final: 0.8246 (tpp) REVERT: A 1097 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 1484 MET cc_start: 0.6035 (ptp) cc_final: 0.5488 (ptm) REVERT: B 465 TYR cc_start: 0.7995 (m-80) cc_final: 0.7747 (m-80) REVERT: B 754 MET cc_start: 0.8499 (tpp) cc_final: 0.8115 (mpp) REVERT: B 1182 GLU cc_start: 0.8402 (pp20) cc_final: 0.8147 (tt0) REVERT: D 73 THR cc_start: 0.5433 (m) cc_final: 0.4608 (p) REVERT: D 137 PHE cc_start: 0.3060 (t80) cc_final: 0.2847 (t80) REVERT: E 151 MET cc_start: 0.8247 (mtp) cc_final: 0.8011 (mtp) REVERT: G 29 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7237 (mmmm) REVERT: G 37 THR cc_start: 0.7027 (p) cc_final: 0.6813 (p) REVERT: G 53 ASN cc_start: 0.5546 (p0) cc_final: 0.5320 (p0) REVERT: G 117 MET cc_start: 0.0671 (mmm) cc_final: 0.0288 (mmm) REVERT: I 46 GLN cc_start: 0.6492 (pp30) cc_final: 0.6267 (pp30) REVERT: I 108 MET cc_start: 0.8624 (mmm) cc_final: 0.7714 (mmm) REVERT: M 133 MET cc_start: 0.6659 (tmm) cc_final: 0.6259 (tmm) REVERT: M 136 GLU cc_start: 0.4115 (pm20) cc_final: 0.3759 (mp0) REVERT: O 72 MET cc_start: 0.6467 (tpp) cc_final: 0.5873 (pmm) REVERT: Z 460 MET cc_start: 0.4417 (tmm) cc_final: 0.3597 (tpp) REVERT: Z 474 MET cc_start: -0.0908 (mmp) cc_final: -0.1540 (mmp) REVERT: Z 481 ILE cc_start: 0.5149 (mt) cc_final: 0.4771 (mt) REVERT: Y 37 ASP cc_start: 0.1579 (m-30) cc_final: 0.0993 (m-30) REVERT: Y 48 MET cc_start: 0.0430 (tmm) cc_final: 0.0064 (ppp) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.5084 time to fit residues: 270.0535 Evaluate side-chains 259 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 0.0060 chunk 175 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 85 optimal weight: 0.0470 chunk 279 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 overall best weight: 3.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS A 804 HIS B 188 ASN C 32 ASN D 61 GLN D 135 HIS D 171 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 GLN O 107 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 39213 Z= 0.269 Angle : 0.550 10.907 53296 Z= 0.283 Chirality : 0.043 0.188 5975 Planarity : 0.004 0.097 6626 Dihedral : 12.344 177.094 5942 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.07 % Allowed : 0.93 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.35 (0.13), residues: 4537 helix: 1.24 (0.14), residues: 1443 sheet: -0.40 (0.18), residues: 782 loop : -0.08 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.005 0.001 HIS A 313 PHE 0.021 0.001 PHE B 499 TYR 0.025 0.001 TYR B 829 ARG 0.006 0.000 ARG I 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 314 time to evaluate : 5.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8625 (tpp) cc_final: 0.8229 (tpp) REVERT: A 565 MET cc_start: 0.8268 (tpp) cc_final: 0.7920 (tpp) REVERT: A 1484 MET cc_start: 0.6010 (ptp) cc_final: 0.5473 (ptm) REVERT: B 754 MET cc_start: 0.8488 (tpp) cc_final: 0.8096 (mpp) REVERT: D 73 THR cc_start: 0.5284 (m) cc_final: 0.4649 (p) REVERT: D 137 PHE cc_start: 0.2854 (t80) cc_final: 0.2644 (t80) REVERT: E 151 MET cc_start: 0.8260 (mtp) cc_final: 0.8030 (mtp) REVERT: G 29 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7794 (mmmm) REVERT: G 37 THR cc_start: 0.7019 (p) cc_final: 0.6742 (p) REVERT: G 53 ASN cc_start: 0.5502 (p0) cc_final: 0.5165 (p0) REVERT: I 46 GLN cc_start: 0.6558 (pp30) cc_final: 0.6318 (pp30) REVERT: I 108 MET cc_start: 0.8625 (mmm) cc_final: 0.7745 (mmm) REVERT: M 133 MET cc_start: 0.6592 (tmm) cc_final: 0.5955 (tmm) REVERT: M 136 GLU cc_start: 0.4158 (pm20) cc_final: 0.3851 (mp0) REVERT: O 72 MET cc_start: 0.6425 (tpp) cc_final: 0.5758 (pmm) REVERT: Z 460 MET cc_start: 0.4176 (tmm) cc_final: 0.3516 (tpp) REVERT: Z 474 MET cc_start: -0.0917 (mmp) cc_final: -0.1535 (mmp) REVERT: Z 481 ILE cc_start: 0.5166 (mt) cc_final: 0.4790 (mt) REVERT: Y 37 ASP cc_start: 0.2000 (m-30) cc_final: 0.1405 (m-30) REVERT: Y 48 MET cc_start: 0.0535 (tmm) cc_final: 0.0177 (ppp) REVERT: Y 64 MET cc_start: 0.4437 (pmm) cc_final: 0.4201 (pmm) outliers start: 2 outliers final: 0 residues processed: 314 average time/residue: 0.5292 time to fit residues: 272.7959 Evaluate side-chains 251 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 384 optimal weight: 9.9990 chunk 409 optimal weight: 5.9990 chunk 420 optimal weight: 40.0000 chunk 246 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 370 optimal weight: 2.9990 chunk 387 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 72 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 595 HIS D 171 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 39213 Z= 0.440 Angle : 0.660 12.900 53296 Z= 0.338 Chirality : 0.045 0.192 5975 Planarity : 0.005 0.114 6626 Dihedral : 12.460 175.494 5942 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 4537 helix: 1.01 (0.14), residues: 1451 sheet: -0.50 (0.18), residues: 755 loop : -0.19 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.003 TRP A 988 HIS 0.011 0.001 HIS A 599 PHE 0.025 0.002 PHE A 458 TYR 0.038 0.002 TYR B 829 ARG 0.009 0.001 ARG I 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 4.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8672 (tpp) cc_final: 0.8465 (tpp) REVERT: A 1484 MET cc_start: 0.6194 (ptp) cc_final: 0.5606 (ptm) REVERT: B 754 MET cc_start: 0.8588 (tpp) cc_final: 0.8079 (tpp) REVERT: D 73 THR cc_start: 0.5625 (m) cc_final: 0.5030 (p) REVERT: D 137 PHE cc_start: 0.3028 (t80) cc_final: 0.2747 (t80) REVERT: E 151 MET cc_start: 0.8345 (mtp) cc_final: 0.8104 (mtp) REVERT: E 210 GLN cc_start: 0.6826 (pt0) cc_final: 0.6613 (pt0) REVERT: G 29 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7883 (mmmm) REVERT: G 37 THR cc_start: 0.7103 (p) cc_final: 0.6826 (p) REVERT: I 46 GLN cc_start: 0.6852 (pp30) cc_final: 0.6569 (pp30) REVERT: M 121 LYS cc_start: 0.6527 (tptp) cc_final: 0.6161 (tptp) REVERT: M 133 MET cc_start: 0.6519 (tmm) cc_final: 0.5649 (tmm) REVERT: M 136 GLU cc_start: 0.4052 (pm20) cc_final: 0.3605 (mp0) REVERT: O 72 MET cc_start: 0.6726 (tpp) cc_final: 0.6049 (pmm) REVERT: Z 460 MET cc_start: 0.4211 (tmm) cc_final: 0.3457 (tpp) REVERT: Z 481 ILE cc_start: 0.5203 (mt) cc_final: 0.4815 (mt) REVERT: Y 37 ASP cc_start: 0.2001 (m-30) cc_final: 0.1536 (m-30) REVERT: Y 48 MET cc_start: 0.0377 (tmm) cc_final: 0.0077 (ppp) REVERT: Y 64 MET cc_start: 0.4651 (pmm) cc_final: 0.4312 (pmm) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.5358 time to fit residues: 262.2722 Evaluate side-chains 238 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 0.8980 chunk 268 optimal weight: 8.9990 chunk 433 optimal weight: 0.0970 chunk 264 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 454 optimal weight: 0.9990 chunk 418 optimal weight: 50.0000 chunk 361 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 279 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 HIS B 188 ASN B1007 GLN C 32 ASN C 51 GLN D 61 GLN D 171 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 GLN O 51 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39213 Z= 0.172 Angle : 0.546 11.757 53296 Z= 0.281 Chirality : 0.043 0.189 5975 Planarity : 0.004 0.109 6626 Dihedral : 12.390 176.098 5942 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.29 (0.13), residues: 4537 helix: 1.17 (0.14), residues: 1446 sheet: -0.41 (0.18), residues: 764 loop : -0.13 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 988 HIS 0.004 0.001 HIS A 465 PHE 0.045 0.001 PHE A 458 TYR 0.024 0.001 TYR B 843 ARG 0.005 0.000 ARG B 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9074 Ramachandran restraints generated. 4537 Oldfield, 0 Emsley, 4537 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8647 (tpp) cc_final: 0.8346 (tpp) REVERT: A 524 MET cc_start: 0.7343 (mmm) cc_final: 0.7111 (mmm) REVERT: A 565 MET cc_start: 0.8368 (tpp) cc_final: 0.7920 (tpp) REVERT: A 1097 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 1484 MET cc_start: 0.6114 (ptp) cc_final: 0.5510 (ptm) REVERT: B 754 MET cc_start: 0.8425 (tpp) cc_final: 0.8172 (mpp) REVERT: D 73 THR cc_start: 0.5415 (m) cc_final: 0.4796 (p) REVERT: D 137 PHE cc_start: 0.2978 (t80) cc_final: 0.2726 (t80) REVERT: E 151 MET cc_start: 0.8287 (mtp) cc_final: 0.8034 (mtp) REVERT: E 210 GLN cc_start: 0.6803 (pt0) cc_final: 0.6576 (pt0) REVERT: G 29 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7706 (mmmm) REVERT: G 37 THR cc_start: 0.6971 (p) cc_final: 0.6721 (p) REVERT: M 133 MET cc_start: 0.6535 (tmm) cc_final: 0.5732 (tmm) REVERT: M 136 GLU cc_start: 0.3956 (pm20) cc_final: 0.3748 (mp0) REVERT: O 72 MET cc_start: 0.6514 (tpp) cc_final: 0.6212 (pmm) REVERT: Z 460 MET cc_start: 0.4272 (tmm) cc_final: 0.3565 (tpp) REVERT: Z 481 ILE cc_start: 0.5195 (mt) cc_final: 0.4838 (mt) REVERT: Y 37 ASP cc_start: 0.1981 (m-30) cc_final: 0.1581 (m-30) REVERT: Y 48 MET cc_start: 0.0570 (tmm) cc_final: 0.0193 (ppp) REVERT: Y 64 MET cc_start: 0.4831 (pmm) cc_final: 0.4527 (pmm) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.5167 time to fit residues: 266.3061 Evaluate side-chains 250 residues out of total 4068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 9.9990 chunk 287 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 333 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 372 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN C 51 GLN D 90 ASN D 171 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN M 140 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.069548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.044124 restraints weight = 242469.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.046203 restraints weight = 122049.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.046911 restraints weight = 76658.195| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39213 Z= 0.285 Angle : 0.569 11.614 53296 Z= 0.293 Chirality : 0.044 0.203 5975 Planarity : 0.004 0.106 6626 Dihedral : 12.359 175.119 5942 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.05 % Allowed : 0.34 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.02 % Twisted Proline : 0.47 % 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: 0.26 (0.13), residues: 4537 helix: 1.12 (0.14), residues: 1460 sheet: -0.47 (0.18), residues: 773 loop : -0.11 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 988 HIS 0.004 0.001 HIS G 9 PHE 0.036 0.001 PHE A 458 TYR 0.025 0.001 TYR B 829 ARG 0.006 0.000 ARG I 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7340.29 seconds wall clock time: 135 minutes 27.44 seconds (8127.44 seconds total)