Starting phenix.real_space_refine (version: dev) on Wed Feb 22 14:46:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/02_2023/6o7h_0641.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/02_2023/6o7h_0641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/02_2023/6o7h_0641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/02_2023/6o7h_0641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/02_2023/6o7h_0641.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7h_0641/02_2023/6o7h_0641.pdb" } resolution = 2.9 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 Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 755": "NH1" <-> "NH2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6152 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1047 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Chain: "D" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2265 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "F" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2536 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 15, 'TRANS': 345} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 93, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Chain: "A" 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p_pur': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3079 SG CYS A 389 57.900 85.339 89.908 1.00 26.12 S ATOM 3099 SG CYS A 392 53.925 83.414 90.176 1.00 20.38 S ATOM 3254 SG CYS A 413 55.553 86.020 92.716 1.00 30.17 S ATOM 3274 SG CYS A 416 56.496 82.553 92.693 1.00 30.70 S ATOM 8026 SG CYS C 113 73.888 99.035 65.322 1.00 24.94 S ATOM 8093 SG CYS C 122 74.316 98.299 61.726 1.00 18.20 S ATOM 8113 SG CYS C 125 71.610 95.804 64.201 1.00 17.21 S ATOM 10291 SG CYS D 113 93.830 71.709 67.401 1.00 32.50 S ATOM 10358 SG CYS D 122 96.213 71.721 64.605 1.00 31.10 S ATOM 10378 SG CYS D 125 91.608 70.721 64.658 1.00 23.12 S Time building chain proxies: 10.32, per 1000 atoms: 0.59 Number of scatterers: 17576 At special positions: 0 Unit cell: (127.413, 119.79, 150.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 49 16.00 P 50 15.00 O 3377 8.00 N 3083 7.00 C 11014 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: 6.94 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 29 sheets defined 42.3% alpha, 15.8% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 4.77 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.557A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.893A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.778A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.591A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.764A pdb=" N PHE A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.507A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 171 through 184 Proline residue: A 177 - end of helix removed outlier: 3.730A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 255 through 282 removed outlier: 3.557A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.697A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.572A pdb=" N LYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.733A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.854A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.663A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.664A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.737A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.877A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.897A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.839A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 4.526A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.355A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.309A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.835A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 removed outlier: 4.203A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.555A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.861A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 3.616A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 4.019A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.787A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.609A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.967A pdb=" N LEU C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.509A pdb=" N TRP C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.919A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.585A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.617A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 70 removed outlier: 3.799A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.641A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 247 through 254 removed outlier: 4.032A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.905A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.865A pdb=" N GLU D 284 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'E' and resid 20 through 36 Processing helix chain 'E' and resid 37 through 50 removed outlier: 3.888A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.919A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 removed outlier: 3.569A pdb=" N ARG E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.845A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.554A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.755A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.591A pdb=" N UNK F 46 " --> pdb=" O UNK F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 4.304A pdb=" N UNK F 58 " --> pdb=" O UNK F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 132 removed outlier: 3.572A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.815A pdb=" N UNK F 141 " --> pdb=" O UNK F 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK F 142 " --> pdb=" O UNK F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 151 through 155 removed outlier: 4.183A pdb=" N UNK F 155 " --> pdb=" O UNK F 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 155' Processing helix chain 'F' and resid 160 through 169 removed outlier: 4.251A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK F 169 " --> pdb=" O UNK F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.935A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.677A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.564A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.837A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 4.113A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.313A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.224A pdb=" N LEU A 119 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.708A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA5, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 4.265A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 430 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 586 removed outlier: 7.044A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 622 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.675A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.887A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.792A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.706A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.726A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.612A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 7.392A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 169 Processing sheet with id=AC1, first strand: chain 'D' and resid 231 through 232 removed outlier: 7.294A pdb=" N GLY D 232 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL F 211 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.252A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 134 removed outlier: 3.646A pdb=" N VAL E 127 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 252 through 254 removed outlier: 4.608A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.535A pdb=" N LEU E 230 " --> pdb=" O PHE E 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC9, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.565A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.718A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4576 1.33 - 1.45: 3644 1.45 - 1.57: 9655 1.57 - 1.69: 97 1.69 - 1.81: 80 Bond restraints: 18052 Sorted by residual: bond pdb=" C5 A K 3 " pdb=" C6 A K 3 " ideal model delta sigma weight residual 1.406 1.324 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C5 A K 1 " pdb=" C6 A K 1 " ideal model delta sigma weight residual 1.406 1.328 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 A K 4 " pdb=" C6 A K 4 " ideal model delta sigma weight residual 1.406 1.329 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 1.593 1.649 -0.056 1.50e-02 4.44e+03 1.37e+01 bond pdb=" C5 A K 2 " pdb=" C6 A K 2 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 18047 not shown) Histogram of bond angle deviations from ideal: 83.50 - 93.66: 5 93.66 - 103.82: 365 103.82 - 113.97: 10326 113.97 - 124.13: 13080 124.13 - 134.29: 863 Bond angle restraints: 24639 Sorted by residual: angle pdb=" O3' A K 2 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 104.00 85.62 18.38 1.50e+00 4.44e-01 1.50e+02 angle pdb=" OP2 A K 3 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 108.00 83.50 24.50 3.00e+00 1.11e-01 6.67e+01 angle pdb=" OP1 A K 1 " pdb=" P A K 1 " pdb=" O5' A K 1 " ideal model delta sigma weight residual 108.00 87.41 20.59 3.00e+00 1.11e-01 4.71e+01 angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N PRO B 33 " pdb=" CA PRO B 33 " pdb=" CB PRO B 33 " ideal model delta sigma weight residual 103.25 110.20 -6.95 1.05e+00 9.07e-01 4.38e+01 ... (remaining 24634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 10464 34.35 - 68.70: 155 68.70 - 103.05: 12 103.05 - 137.40: 0 137.40 - 171.74: 3 Dihedral angle restraints: 10634 sinusoidal: 4564 harmonic: 6070 Sorted by residual: dihedral pdb=" O4' C G 11 " pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sinusoidal sigma weight residual -128.00 43.74 -171.74 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 5 " pdb=" C1' C G 5 " pdb=" N1 C G 5 " pdb=" C2 C G 5 " ideal model delta sinusoidal sigma weight residual -128.00 30.12 -158.12 1 1.70e+01 3.46e-03 6.40e+01 dihedral pdb=" C4' A K 2 " pdb=" O4' A K 2 " pdb=" C1' A K 2 " pdb=" C2' A K 2 " ideal model delta sinusoidal sigma weight residual -21.00 26.55 -47.55 1 8.00e+00 1.56e-02 4.88e+01 ... (remaining 10631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2492 0.116 - 0.231: 216 0.231 - 0.347: 13 0.347 - 0.463: 1 0.463 - 0.579: 2 Chirality restraints: 2724 Sorted by residual: chirality pdb=" P A K 1 " pdb=" OP1 A K 1 " pdb=" OP2 A K 1 " pdb=" O5' A K 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" P A K 3 " pdb=" OP1 A K 3 " pdb=" OP2 A K 3 " pdb=" O5' A K 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C1' C G 5 " pdb=" O4' C G 5 " pdb=" C2' C G 5 " pdb=" N1 C G 5 " both_signs ideal model delta sigma weight residual False 2.45 2.10 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 2721 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 252 " 0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C GLY A 252 " -0.091 2.00e-02 2.50e+03 pdb=" O GLY A 252 " 0.035 2.00e-02 2.50e+03 pdb=" N LYS A 253 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 71 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C MET A 71 " 0.077 2.00e-02 2.50e+03 pdb=" O MET A 71 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE A 72 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 47 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ALA E 47 " 0.076 2.00e-02 2.50e+03 pdb=" O ALA E 47 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE E 48 " -0.025 2.00e-02 2.50e+03 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 10 2.26 - 2.92: 6851 2.92 - 3.58: 23617 3.58 - 4.24: 42811 4.24 - 4.90: 71232 Nonbonded interactions: 144521 Sorted by model distance: nonbonded pdb=" O3' C H 35 " pdb=" P G H 101 " model vdw 1.596 3.400 nonbonded pdb=" P A K 1 " pdb=" O3' A K 4 " model vdw 1.628 3.400 nonbonded pdb=" O2' A K 1 " pdb=" OP1 A K 2 " model vdw 2.055 2.440 nonbonded pdb=" O5' A K 1 " pdb=" O3' A K 4 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU A 180 " pdb=" OH TYR A 547 " model vdw 2.204 2.440 ... (remaining 144516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 4 through 26 or resid 34 through 287 or resid 301)) selection = (chain 'D' and (resid 4 through 26 or resid 34 through 287 or resid 301)) } 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 50 5.49 5 S 49 5.16 5 C 11014 2.51 5 N 3083 2.21 5 O 3377 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.010 Extract box with map and model: 4.730 Check model and map are aligned: 0.270 Process input model: 52.310 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.006 0.082 18052 Z= 0.415 Angle : 1.105 24.503 24639 Z= 0.653 Chirality : 0.067 0.579 2724 Planarity : 0.007 0.061 2993 Dihedral : 12.419 171.744 6752 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.15), residues: 2006 helix: -3.61 (0.12), residues: 771 sheet: -1.95 (0.26), residues: 302 loop : -2.43 (0.17), residues: 933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 445 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 460 average time/residue: 1.4990 time to fit residues: 756.8523 Evaluate side-chains 271 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 2.6063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 456 GLN A 668 HIS B 72 ASN C 37 ASN C 179 ASN D 22 HIS D 83 ASN D 106 ASN D 179 ASN D 183 ASN F 18 ASN F 33 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18052 Z= 0.200 Angle : 0.632 15.251 24639 Z= 0.327 Chirality : 0.044 0.198 2724 Planarity : 0.005 0.053 2993 Dihedral : 11.554 178.489 2932 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.16), residues: 2006 helix: -1.70 (0.16), residues: 778 sheet: -1.43 (0.27), residues: 298 loop : -2.12 (0.18), residues: 930 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 293 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 19 residues processed: 327 average time/residue: 1.4616 time to fit residues: 529.0926 Evaluate side-chains 274 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 255 time to evaluate : 1.948 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 7 average time/residue: 0.2286 time to fit residues: 5.3738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 18052 Z= 0.234 Angle : 0.597 14.904 24639 Z= 0.307 Chirality : 0.044 0.193 2724 Planarity : 0.005 0.050 2993 Dihedral : 11.349 177.530 2932 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2006 helix: -0.67 (0.18), residues: 783 sheet: -1.02 (0.28), residues: 296 loop : -1.92 (0.18), residues: 927 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 260 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 20 residues processed: 312 average time/residue: 1.4105 time to fit residues: 489.4681 Evaluate side-chains 263 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.2535 time to fit residues: 5.0551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 77 optimal weight: 0.0170 chunk 108 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18052 Z= 0.163 Angle : 0.540 14.598 24639 Z= 0.276 Chirality : 0.042 0.196 2724 Planarity : 0.004 0.047 2993 Dihedral : 11.163 177.419 2932 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.18), residues: 2006 helix: -0.06 (0.18), residues: 787 sheet: -0.84 (0.29), residues: 295 loop : -1.75 (0.19), residues: 924 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 22 residues processed: 304 average time/residue: 1.4690 time to fit residues: 495.2936 Evaluate side-chains 267 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 5 average time/residue: 0.2988 time to fit residues: 5.1365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS D 106 ASN E 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 18052 Z= 0.370 Angle : 0.661 14.243 24639 Z= 0.335 Chirality : 0.047 0.220 2724 Planarity : 0.005 0.074 2993 Dihedral : 11.326 176.617 2932 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.18), residues: 2006 helix: -0.00 (0.19), residues: 788 sheet: -0.81 (0.28), residues: 317 loop : -1.78 (0.19), residues: 901 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 245 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 31 residues processed: 294 average time/residue: 1.4822 time to fit residues: 482.6852 Evaluate side-chains 262 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 0.2425 time to fit residues: 4.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.0870 chunk 34 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 18052 Z= 0.174 Angle : 0.562 14.273 24639 Z= 0.283 Chirality : 0.042 0.203 2724 Planarity : 0.004 0.067 2993 Dihedral : 11.137 176.641 2932 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2006 helix: 0.44 (0.19), residues: 789 sheet: -0.66 (0.28), residues: 303 loop : -1.53 (0.19), residues: 914 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 26 residues processed: 294 average time/residue: 1.4265 time to fit residues: 464.7439 Evaluate side-chains 260 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 2.039 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.2238 time to fit residues: 5.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.0060 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 18052 Z= 0.257 Angle : 0.604 14.066 24639 Z= 0.305 Chirality : 0.044 0.190 2724 Planarity : 0.005 0.085 2993 Dihedral : 11.173 176.963 2932 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2006 helix: 0.47 (0.19), residues: 788 sheet: -0.65 (0.27), residues: 317 loop : -1.54 (0.20), residues: 901 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 27 residues processed: 280 average time/residue: 1.4714 time to fit residues: 457.9949 Evaluate side-chains 262 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 235 time to evaluate : 1.780 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 0.2596 time to fit residues: 3.1946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18052 Z= 0.198 Angle : 0.573 14.059 24639 Z= 0.289 Chirality : 0.043 0.195 2724 Planarity : 0.004 0.047 2993 Dihedral : 11.092 176.735 2932 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2006 helix: 0.70 (0.19), residues: 777 sheet: -0.65 (0.27), residues: 317 loop : -1.45 (0.20), residues: 912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 243 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 279 average time/residue: 1.4069 time to fit residues: 436.6691 Evaluate side-chains 254 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 4 average time/residue: 0.5775 time to fit residues: 5.4981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 0.0170 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 144 optimal weight: 0.1980 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 18052 Z= 0.135 Angle : 0.543 13.426 24639 Z= 0.271 Chirality : 0.041 0.221 2724 Planarity : 0.004 0.046 2993 Dihedral : 10.969 177.036 2932 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 2006 helix: 1.01 (0.19), residues: 777 sheet: -0.54 (0.28), residues: 303 loop : -1.40 (0.20), residues: 926 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 21 residues processed: 279 average time/residue: 1.4974 time to fit residues: 461.9697 Evaluate side-chains 250 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 1.894 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 2.0270 time to fit residues: 7.3251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 0.0870 chunk 141 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 18052 Z= 0.189 Angle : 0.573 13.367 24639 Z= 0.286 Chirality : 0.043 0.395 2724 Planarity : 0.004 0.050 2993 Dihedral : 10.942 177.178 2932 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 2006 helix: 1.01 (0.19), residues: 786 sheet: -0.58 (0.27), residues: 319 loop : -1.39 (0.20), residues: 901 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 264 average time/residue: 1.4433 time to fit residues: 424.3227 Evaluate side-chains 242 residues out of total 1723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 1.816 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 2.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.174364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.126313 restraints weight = 19436.756| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.20 r_work: 0.3044 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 18052 Z= 0.188 Angle : 0.572 13.246 24639 Z= 0.284 Chirality : 0.043 0.252 2724 Planarity : 0.004 0.048 2993 Dihedral : 10.908 176.864 2932 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 2006 helix: 1.09 (0.19), residues: 779 sheet: -0.54 (0.27), residues: 317 loop : -1.36 (0.20), residues: 910 =============================================================================== Job complete usr+sys time: 7441.59 seconds wall clock time: 131 minutes 53.22 seconds (7913.22 seconds total)