Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:16:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ol0_12974/12_2022/7ol0_12974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ol0_12974/12_2022/7ol0_12974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ol0_12974/12_2022/7ol0_12974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ol0_12974/12_2022/7ol0_12974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ol0_12974/12_2022/7ol0_12974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ol0_12974/12_2022/7ol0_12974.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 219": "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 514": "OE1" <-> "OE2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A GLU 824": "OE1" <-> "OE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 869": "OE1" <-> "OE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 936": "OE1" <-> "OE2" Residue "A GLU 951": "OE1" <-> "OE2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A ARG 1052": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" 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 1126": "OE1" <-> "OE2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1302": "OE1" <-> "OE2" Residue "A GLU 1364": "OE1" <-> "OE2" Residue "A ARG 1408": "NH1" <-> "NH2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 137": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 628": "OE1" <-> "OE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 845": "NH1" <-> "NH2" Residue "B GLU 848": "OE1" <-> "OE2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B GLU 895": "OE1" <-> "OE2" Residue "B ARG 936": "NH1" <-> "NH2" Residue "B GLU 991": "OE1" <-> "OE2" Residue "B GLU 1029": "OE1" <-> "OE2" Residue "B GLU 1103": "OE1" <-> "OE2" Residue "B GLU 1167": "OE1" <-> "OE2" Residue "B GLU 1186": "OE1" <-> "OE2" Residue "B ARG 1208": "NH1" <-> "NH2" Residue "B GLU 1213": "OE1" <-> "OE2" Residue "B GLU 1238": "OE1" <-> "OE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L ARG 51": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32892 Number of models: 1 Model: "" Number of chains: 22 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: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2068 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 926 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 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: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Z" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 393 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} 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: "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: "T" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 472 SG CYS A 71 106.569 77.670 76.639 1.00 53.88 S ATOM 494 SG CYS A 74 105.007 80.870 78.101 1.00 51.65 S ATOM 541 SG CYS A 81 102.887 77.697 77.856 1.00 47.27 S ATOM 776 SG CYS A 111 87.497 84.600 33.386 1.00 72.60 S ATOM 804 SG CYS A 114 89.614 87.543 33.425 1.00 75.57 S ATOM 1117 SG CYS A 154 85.969 87.611 31.767 1.00 81.24 S ATOM 1144 SG CYS A 184 88.997 85.785 30.150 1.00 78.86 S ATOM 19765 SG CYS B1196 99.763 93.113 68.722 1.00 50.70 S ATOM 19787 SG CYS B1199 98.218 90.188 66.804 1.00 49.13 S ATOM 19902 SG CYS B1214 101.687 89.862 67.987 1.00 64.85 S ATOM 19923 SG CYS B1217 100.822 92.263 65.112 1.00 65.67 S ATOM 20890 SG CYS C 88 83.056 56.214 137.822 1.00 45.58 S ATOM 20903 SG CYS C 90 85.671 54.722 135.250 1.00 49.65 S ATOM 20934 SG CYS C 94 84.329 52.979 138.255 1.00 35.53 S ATOM 20956 SG CYS C 97 82.103 53.550 135.143 1.00 32.77 S ATOM 28719 SG CYS I 86 18.992 29.905 56.976 1.00 54.12 S ATOM 28743 SG CYS I 89 18.821 26.069 57.828 1.00 57.57 S ATOM 28947 SG CYS I 114 21.598 28.235 59.174 1.00 40.67 S ATOM 28982 SG CYS I 119 21.427 27.291 55.551 1.00 54.61 S ATOM 28173 SG CYS I 17 45.657 34.797 22.009 1.00 57.52 S ATOM 28197 SG CYS I 20 49.210 35.613 23.360 1.00 61.55 S ATOM 28348 SG CYS I 39 47.496 38.102 21.496 1.00 55.85 S ATOM 28367 SG CYS I 42 48.905 34.886 19.818 1.00 67.40 S ATOM 29092 SG CYS J 7 56.902 45.435 118.650 1.00 30.76 S ATOM 29116 SG CYS J 10 55.978 46.550 122.230 1.00 19.20 S ATOM 29380 SG CYS J 44 53.364 46.560 119.338 1.00 22.24 S ATOM 29386 SG CYS J 45 54.599 43.539 121.119 1.00 20.46 S ATOM 30523 SG CYS L 19 92.292 26.372 100.431 1.00 40.79 S ATOM 30542 SG CYS L 22 92.630 23.458 102.811 1.00 46.36 S ATOM 30659 SG CYS L 36 95.613 24.716 101.128 1.00 49.32 S ATOM 30685 SG CYS L 39 92.720 22.921 99.081 1.00 51.95 S Time building chain proxies: 18.48, per 1000 atoms: 0.56 Number of scatterers: 32892 At special positions: 0 Unit cell: (159.6, 149.1, 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 8 29.99 S 197 16.00 P 79 15.00 Mg 1 11.99 O 6322 8.00 N 5776 7.00 C 20509 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: 13.96 Conformation dependent library (CDL) restraints added in 4.4 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 71 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb=" ZN A2003 " 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 114 " 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 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 20 " 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 J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " 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 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 45 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7358 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 49 sheets defined 37.8% alpha, 19.7% beta 29 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.33 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.700A 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 Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 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 488 through 493 removed outlier: 3.569A 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 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: 3.662A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.593A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.880A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.574A 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 Processing helix chain 'A' and resid 926 through 934 removed outlier: 4.174A pdb=" N ARG A 932 " --> pdb=" O ARG A 928 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 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 1018 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 1101 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.700A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1148 removed outlier: 3.628A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1166 through 1169 No H-bonds generated for 'chain 'A' and resid 1166 through 1169' Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.645A pdb=" N THR A1184 " --> pdb=" O PRO A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 3.761A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 4.475A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.825A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1431 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 4.027A 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 1478 through 1483 removed outlier: 3.697A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1483' Processing helix chain 'B' and resid 98 through 115 removed outlier: 3.887A pdb=" N TRP B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 130 through 138 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 385 removed outlier: 3.899A pdb=" N MET B 375 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 378 " --> pdb=" O MET B 374 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 423 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: 3.734A pdb=" N GLY B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 514 through 528 removed outlier: 3.582A pdb=" N SER B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.788A pdb=" N ALA B 536 " --> pdb=" O GLN B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 559 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 624 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.895A pdb=" N ALA B 639 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 671 Processing helix chain 'B' and resid 713 through 721 Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 729 through 735 Processing helix 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: 3.636A pdb=" N ILE B 780 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 781 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 794 Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.514A pdb=" N ASN B 799 " --> pdb=" O GLN B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 843 removed outlier: 3.652A 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 1046 through 1049 Processing helix chain 'B' and resid 1054 through 1071 removed outlier: 3.916A 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: 3.580A pdb=" N ARG B1157 " --> pdb=" O GLY B1154 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B1158 " --> pdb=" O ARG B1155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1154 through 1158' Processing helix chain 'B' and resid 1164 through 1175 Processing helix chain 'B' and resid 1176 through 1185 Processing helix chain 'B' and resid 1230 through 1241 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.522A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.565A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) 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 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.550A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 Processing helix chain 'D' and resid 65 through 69 removed outlier: 3.651A pdb=" N GLU D 69 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.645A pdb=" N TYR D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.010A pdb=" N ALA D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.616A pdb=" N ILE D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 180 removed outlier: 3.967A pdb=" N GLN D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.684A pdb=" N THR E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG E 9 " --> pdb=" O GLU E 5 " (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 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 34 removed outlier: 3.514A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 114 through 118 removed outlier: 3.950A pdb=" N GLU G 118 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.863A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER I 73 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN I 74 " --> pdb=" O ASP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 107 removed outlier: 4.017A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA I 107 " --> pdb=" O ALA I 104 " (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: 3.779A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.660A 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: 3.706A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.962A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP K 53 " --> pdb=" O GLN K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 95 removed outlier: 6.781A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.145A 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: 4.213A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA6, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.706A pdb=" N LEU B1161 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1137 through 1139 removed outlier: 3.551A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.739A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.829A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AB2, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.128A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.715A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB6, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB7, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.723A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1165 Processing sheet with id=AB9, first strand: chain 'A' and resid 1243 through 1244 Processing sheet with id=AC1, first strand: chain 'A' and resid 1243 through 1244 removed outlier: 4.722A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AC3, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.120A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR G 72 " --> pdb=" O LEU G 7 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.120A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR G 50 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 142 through 143 removed outlier: 3.522A pdb=" N LYS B 164 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP B 204 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR B 202 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B 170 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 227 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 203 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N PHE B 225 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE B 205 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS B 223 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LYS B 207 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N HIS B 221 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 209 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 219 " --> pdb=" O VAL B 209 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AC7, first strand: chain 'B' and resid 262 through 264 Processing sheet with id=AC8, first strand: chain 'B' and resid 468 through 471 Processing sheet with id=AC9, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.683A pdb=" N TYR B 294 " --> pdb=" O MET B 316 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD2, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD3, first strand: chain 'B' and resid 628 through 629 removed outlier: 5.407A pdb=" N TRP B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 646 " --> pdb=" O TRP B 650 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 652 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS B 643 " --> pdb=" O ILE B 689 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE B 691 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N PHE B 645 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.141A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B1001 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 981 " --> pdb=" O ARG B1001 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL B1003 " --> pdb=" O GLY B 979 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY B 979 " --> pdb=" O VAL B1003 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 824 through 828 removed outlier: 4.141A pdb=" N LYS B 994 " --> pdb=" O GLU B 895 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B1001 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL B 981 " --> pdb=" O ARG B1001 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL B1003 " --> pdb=" O GLY B 979 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N GLY B 979 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 984 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 836 through 837 Processing sheet with id=AD7, first strand: chain 'B' and resid 1102 through 1103 removed outlier: 7.110A pdb=" N VAL B 871 " --> pdb=" O GLY B1023 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B1025 " --> pdb=" O VAL B 871 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET B 873 " --> pdb=" O GLN B1025 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ILE B1042 " --> pdb=" O ASN B 854 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE B 856 " --> pdb=" O ILE B1042 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE B1044 " --> pdb=" O ILE B 856 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 858 " --> pdb=" O ILE B1044 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE B1119 " --> pdb=" O ILE B 859 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 904 through 906 Processing sheet with id=AD9, first strand: chain 'B' and resid 942 through 944 removed outlier: 6.971A pdb=" N THR B 971 " --> pdb=" O ILE B 943 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1190 through 1196 Processing sheet with id=AE2, first strand: chain 'B' and resid 1204 through 1206 Processing sheet with id=AE3, first strand: chain 'C' and resid 8 through 14 removed outlier: 5.673A pdb=" N VAL C 9 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU C 24 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ILE C 11 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 22 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.606A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.285A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.859A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 81 through 82 Processing sheet with id=AE8, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.271A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 84 through 89 removed outlier: 4.171A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 160 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AF2, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AF4, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.688A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 1353 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 16.35 Time building geometry restraints manager: 15.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6083 1.32 - 1.44: 8339 1.44 - 1.57: 18779 1.57 - 1.69: 154 1.69 - 1.82: 311 Bond restraints: 33666 Sorted by residual: bond pdb=" C GLN A 539 " pdb=" O GLN A 539 " ideal model delta sigma weight residual 1.242 1.198 0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" CB ARG B 936 " pdb=" CG ARG B 936 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.61e+00 bond pdb=" N ARG E 162 " pdb=" CA ARG E 162 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.79e+00 bond pdb=" CB MET I 108 " pdb=" CG MET I 108 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" N VAL A 538 " pdb=" CA VAL A 538 " ideal model delta sigma weight residual 1.456 1.481 -0.026 1.11e-02 8.12e+03 5.31e+00 ... (remaining 33661 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.52: 626 103.52 - 111.17: 13312 111.17 - 118.83: 13915 118.83 - 126.48: 17324 126.48 - 134.14: 636 Bond angle restraints: 45813 Sorted by residual: angle pdb=" N ILE B 673 " pdb=" CA ILE B 673 " pdb=" C ILE B 673 " ideal model delta sigma weight residual 112.96 107.92 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N GLU A 961 " pdb=" CA GLU A 961 " pdb=" CB GLU A 961 " ideal model delta sigma weight residual 110.28 117.77 -7.49 1.55e+00 4.16e-01 2.34e+01 angle pdb=" N VAL G 148 " pdb=" CA VAL G 148 " pdb=" C VAL G 148 " ideal model delta sigma weight residual 113.71 109.35 4.36 9.50e-01 1.11e+00 2.11e+01 angle pdb=" CA LEU A 486 " pdb=" CB LEU A 486 " pdb=" CG LEU A 486 " ideal model delta sigma weight residual 116.30 100.77 15.53 3.50e+00 8.16e-02 1.97e+01 angle pdb=" C ARG A1375 " pdb=" CA ARG A1375 " pdb=" CB ARG A1375 " ideal model delta sigma weight residual 110.85 103.47 7.38 1.70e+00 3.46e-01 1.88e+01 ... (remaining 45808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 19763 35.42 - 70.83: 547 70.83 - 106.25: 42 106.25 - 141.67: 0 141.67 - 177.09: 1 Dihedral angle restraints: 20353 sinusoidal: 8977 harmonic: 11376 Sorted by residual: dihedral pdb=" CA GLN B 331 " pdb=" C GLN B 331 " pdb=" N ARG B 332 " pdb=" CA ARG B 332 " ideal model delta harmonic sigma weight residual 180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 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 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR A 686 " pdb=" C THR A 686 " pdb=" N ILE A 687 " pdb=" CA ILE A 687 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 20350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4812 0.108 - 0.216: 309 0.216 - 0.325: 7 0.325 - 0.433: 4 0.433 - 0.541: 1 Chirality restraints: 5133 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 2.10 0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CB VAL I 72 " pdb=" CA VAL I 72 " pdb=" CG1 VAL I 72 " pdb=" CG2 VAL I 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 399 " pdb=" CA ILE A 399 " pdb=" CG1 ILE A 399 " pdb=" CG2 ILE A 399 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 5130 not shown) Planarity restraints: 5659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1125 " -0.034 2.00e-02 2.50e+03 3.02e-02 1.82e+01 pdb=" CG TYR B1125 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B1125 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B1125 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B1125 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B1125 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1125 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1125 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 63 " 0.017 2.00e-02 2.50e+03 2.26e-02 8.95e+00 pdb=" CG PHE C 63 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 63 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 63 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 63 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 63 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 64 " -0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO D 65 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 65 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 65 " -0.041 5.00e-02 4.00e+02 ... (remaining 5656 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 427 2.64 - 3.20: 28223 3.20 - 3.77: 53684 3.77 - 4.33: 77413 4.33 - 4.90: 124304 Nonbonded interactions: 284051 Sorted by model distance: nonbonded pdb=" O PHE A1247 " pdb=" OD1 ASN A1248 " model vdw 2.073 3.040 nonbonded pdb=" OD1 ASP A 497 " pdb="MG MG A2001 " model vdw 2.112 2.170 nonbonded pdb=" O3' A P 46 " pdb="MG MG A2001 " model vdw 2.129 2.170 nonbonded pdb=" OD1 ASP A 495 " pdb="MG MG A2001 " model vdw 2.130 2.170 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.204 2.440 ... (remaining 284046 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 79 5.49 5 Mg 1 5.21 5 S 197 5.16 5 C 20509 2.51 5 N 5776 2.21 5 O 6322 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.240 Check model and map are aligned: 0.480 Convert atoms to be neutral: 0.310 Process input model: 102.300 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.010 0.101 33666 Z= 0.619 Angle : 0.878 15.529 45813 Z= 0.482 Chirality : 0.058 0.541 5133 Planarity : 0.006 0.075 5659 Dihedral : 15.669 177.086 12995 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 3864 helix: -1.09 (0.13), residues: 1341 sheet: -0.72 (0.20), residues: 643 loop : -0.80 (0.14), residues: 1880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 523 time to evaluate : 3.896 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 524 average time/residue: 1.6264 time to fit residues: 997.0509 Evaluate side-chains 400 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.892 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 305 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 354 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A1042 ASN A1172 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1102 ASN E 95 GLN E 138 ASN G 21 ASN I 46 GLN K 84 GLN K 89 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 33666 Z= 0.199 Angle : 0.552 11.318 45813 Z= 0.296 Chirality : 0.044 0.225 5133 Planarity : 0.004 0.062 5659 Dihedral : 12.764 173.526 5084 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3864 helix: 0.01 (0.14), residues: 1348 sheet: -0.52 (0.20), residues: 622 loop : -0.60 (0.14), residues: 1894 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 431 time to evaluate : 4.091 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 11 residues processed: 457 average time/residue: 1.5909 time to fit residues: 859.4057 Evaluate side-chains 399 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 388 time to evaluate : 4.191 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.7710 time to fit residues: 10.0047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 294 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 354 optimal weight: 4.9990 chunk 383 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 351 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 284 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1172 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS B 726 ASN B1025 GLN B1098 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN E 138 ASN I 46 GLN K 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 33666 Z= 0.402 Angle : 0.597 11.587 45813 Z= 0.315 Chirality : 0.046 0.235 5133 Planarity : 0.005 0.059 5659 Dihedral : 12.789 178.002 5084 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 3864 helix: 0.28 (0.14), residues: 1358 sheet: -0.68 (0.19), residues: 624 loop : -0.44 (0.14), residues: 1882 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 413 time to evaluate : 4.018 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 29 residues processed: 448 average time/residue: 1.6068 time to fit residues: 848.6169 Evaluate side-chains 426 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 397 time to evaluate : 3.785 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 11 average time/residue: 0.7475 time to fit residues: 16.3830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 10.0000 chunk 266 optimal weight: 0.9980 chunk 184 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 238 optimal weight: 0.7980 chunk 356 optimal weight: 20.0000 chunk 376 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 337 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 780 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN E 138 ASN G 24 ASN H 29 HIS I 46 GLN I 56 ASN K 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 33666 Z= 0.178 Angle : 0.502 8.643 45813 Z= 0.267 Chirality : 0.042 0.284 5133 Planarity : 0.004 0.060 5659 Dihedral : 12.671 171.448 5084 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 3864 helix: 0.79 (0.14), residues: 1350 sheet: -0.59 (0.20), residues: 625 loop : -0.31 (0.14), residues: 1889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 420 time to evaluate : 3.801 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 20 residues processed: 452 average time/residue: 1.5452 time to fit residues: 831.7476 Evaluate side-chains 420 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 400 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.6421 time to fit residues: 9.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 280 optimal weight: 20.0000 chunk 155 optimal weight: 0.6980 chunk 321 optimal weight: 6.9990 chunk 260 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 338 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1248 ASN B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN G 24 ASN I 45 GLN I 46 GLN I 56 ASN K 29 ASN K 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 33666 Z= 0.233 Angle : 0.515 9.186 45813 Z= 0.271 Chirality : 0.043 0.318 5133 Planarity : 0.004 0.058 5659 Dihedral : 12.625 173.106 5084 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3864 helix: 0.96 (0.14), residues: 1352 sheet: -0.53 (0.20), residues: 626 loop : -0.23 (0.15), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 412 time to evaluate : 4.078 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 26 residues processed: 453 average time/residue: 1.5046 time to fit residues: 812.6539 Evaluate side-chains 428 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 402 time to evaluate : 3.559 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.7839 time to fit residues: 13.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 377 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 731 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN A1230 GLN B 188 ASN B 726 ASN E 65 ASN E 138 ASN I 45 GLN I 46 GLN I 56 ASN K 89 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 33666 Z= 0.366 Angle : 0.569 10.830 45813 Z= 0.298 Chirality : 0.046 0.381 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.708 176.339 5084 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 3864 helix: 0.88 (0.14), residues: 1356 sheet: -0.58 (0.19), residues: 627 loop : -0.23 (0.15), residues: 1881 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 412 time to evaluate : 3.833 Fit side-chains outliers start: 70 outliers final: 34 residues processed: 461 average time/residue: 1.5309 time to fit residues: 839.9425 Evaluate side-chains 435 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 401 time to evaluate : 4.011 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 6 average time/residue: 0.5265 time to fit residues: 10.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 275 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 317 optimal weight: 0.4980 chunk 210 optimal weight: 0.9990 chunk 375 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1042 ASN B 447 HIS B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN E 65 ASN E 138 ASN G 24 ASN H 126 GLN I 32 ASN I 45 GLN I 56 ASN K 89 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 33666 Z= 0.161 Angle : 0.498 9.440 45813 Z= 0.263 Chirality : 0.042 0.280 5133 Planarity : 0.004 0.059 5659 Dihedral : 12.611 171.130 5084 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3864 helix: 1.22 (0.14), residues: 1342 sheet: -0.55 (0.20), residues: 616 loop : -0.20 (0.15), residues: 1906 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 420 time to evaluate : 4.431 Fit side-chains outliers start: 56 outliers final: 28 residues processed: 458 average time/residue: 1.5222 time to fit residues: 833.1936 Evaluate side-chains 433 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 405 time to evaluate : 3.951 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 4 average time/residue: 0.4022 time to fit residues: 8.0505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN I 45 GLN I 56 ASN K 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 33666 Z= 0.243 Angle : 0.523 9.242 45813 Z= 0.275 Chirality : 0.043 0.270 5133 Planarity : 0.004 0.056 5659 Dihedral : 12.601 173.571 5084 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3864 helix: 1.20 (0.14), residues: 1343 sheet: -0.57 (0.20), residues: 621 loop : -0.14 (0.15), residues: 1900 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 414 time to evaluate : 4.148 Fit side-chains outliers start: 56 outliers final: 31 residues processed: 450 average time/residue: 1.5924 time to fit residues: 853.6532 Evaluate side-chains 439 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 408 time to evaluate : 3.817 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 5 average time/residue: 0.6104 time to fit residues: 11.0124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 3.9990 chunk 360 optimal weight: 3.9990 chunk 328 optimal weight: 0.0470 chunk 350 optimal weight: 0.6980 chunk 210 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 316 optimal weight: 4.9990 chunk 331 optimal weight: 0.1980 chunk 349 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 ASN ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN E 138 ASN G 24 ASN I 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 33666 Z= 0.149 Angle : 0.493 9.325 45813 Z= 0.259 Chirality : 0.042 0.259 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.517 170.273 5084 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3864 helix: 1.38 (0.15), residues: 1352 sheet: -0.50 (0.20), residues: 621 loop : -0.15 (0.15), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 419 time to evaluate : 4.132 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 26 residues processed: 451 average time/residue: 1.6157 time to fit residues: 867.4190 Evaluate side-chains 431 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 405 time to evaluate : 3.917 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 0.4126 time to fit residues: 6.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 0.5980 chunk 370 optimal weight: 0.0970 chunk 226 optimal weight: 0.8980 chunk 175 optimal weight: 0.0870 chunk 257 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 357 optimal weight: 0.0970 chunk 309 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS A1244 ASN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS G 24 ASN I 45 GLN I 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 33666 Z= 0.143 Angle : 0.490 8.592 45813 Z= 0.257 Chirality : 0.041 0.243 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.416 168.951 5084 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3864 helix: 1.55 (0.15), residues: 1345 sheet: -0.38 (0.20), residues: 618 loop : -0.12 (0.15), residues: 1901 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 428 time to evaluate : 3.929 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 23 residues processed: 454 average time/residue: 1.5762 time to fit residues: 854.0257 Evaluate side-chains 424 residues out of total 3464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 401 time to evaluate : 3.741 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 0.4363 time to fit residues: 5.8833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 2.9990 chunk 329 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 HIS B 188 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 867 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN C 265 HIS E 98 ASN G 60 GLN I 45 GLN I 56 ASN L 26 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.103407 restraints weight = 38578.319| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.04 r_work: 0.2809 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 33666 Z= 0.197 Angle : 0.515 8.446 45813 Z= 0.268 Chirality : 0.042 0.253 5133 Planarity : 0.004 0.057 5659 Dihedral : 12.428 171.026 5084 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3864 helix: 1.55 (0.15), residues: 1336 sheet: -0.38 (0.20), residues: 619 loop : -0.08 (0.15), residues: 1909 =============================================================================== Job complete usr+sys time: 12591.87 seconds wall clock time: 222 minutes 29.49 seconds (13349.49 seconds total)