Starting phenix.real_space_refine on Tue Dec 12 17:00:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/12_2023/7kro_23008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/12_2023/7kro_23008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/12_2023/7kro_23008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/12_2023/7kro_23008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/12_2023/7kro_23008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/12_2023/7kro_23008_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 86 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13642 2.51 5 N 3707 2.21 5 O 4383 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 337": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E ARG 443": "NH1" <-> "NH2" Residue "E TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 443": "NH1" <-> "NH2" Residue "F TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21988 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 30, 'TRANS': 896} Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1424 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "F" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 914 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 38} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 73.888 58.971 122.812 1.00 38.24 S ATOM 2495 SG CYS A 306 74.634 60.042 126.547 1.00 31.54 S ATOM 2527 SG CYS A 310 75.110 56.427 125.385 1.00 44.33 S ATOM 3935 SG CYS A 487 76.891 72.859 108.537 1.00 38.63 S ATOM 5188 SG CYS A 645 77.165 75.182 111.520 1.00 45.39 S ATOM 5194 SG CYS A 646 75.483 71.788 112.024 1.00 43.78 S ATOM 10924 SG CYS E 5 116.902 64.767 51.873 1.00 53.22 S ATOM 10945 SG CYS E 8 120.444 64.603 52.931 1.00 57.87 S ATOM 11083 SG CYS E 26 119.149 68.046 52.383 1.00 57.27 S ATOM 11104 SG CYS E 29 119.574 66.254 49.466 1.00 62.73 S ATOM 11269 SG CYS E 50 101.114 86.502 49.723 1.00 97.32 S ATOM 11299 SG CYS E 55 99.863 86.541 46.164 1.00111.12 S ATOM 11432 SG CYS E 72 102.870 88.588 47.064 1.00106.78 S ATOM 11006 SG CYS E 16 109.047 68.612 45.257 1.00 52.87 S ATOM 11021 SG CYS E 19 108.372 64.927 44.093 1.00 62.83 S ATOM 15526 SG CYS F 5 66.643 74.883 62.030 1.00 81.43 S ATOM 15547 SG CYS F 8 68.614 74.900 58.897 1.00 81.50 S ATOM 15685 SG CYS F 26 68.910 78.000 60.930 1.00 83.74 S ATOM 15706 SG CYS F 29 65.837 77.641 59.405 1.00 92.86 S ATOM 15871 SG CYS F 50 67.340 92.652 82.281 1.00125.84 S ATOM 15901 SG CYS F 55 63.809 93.919 82.685 1.00143.39 S ATOM 16034 SG CYS F 72 66.234 95.897 80.623 1.00127.64 S ATOM 15608 SG CYS F 16 59.677 79.704 68.992 1.00 68.26 S ATOM 15623 SG CYS F 19 57.173 76.750 68.365 1.00 86.69 S Time building chain proxies: 11.39, per 1000 atoms: 0.52 Number of scatterers: 21988 At special positions: 0 Unit cell: (143.775, 160.815, 184.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 86 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4383 8.00 N 3707 7.00 C 13642 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: 8.38 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 22 sheets defined 37.9% alpha, 10.4% beta 33 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 10.66 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 4.052A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 197 removed outlier: 3.888A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 240 through 247 Proline residue: A 243 - end of helix removed outlier: 3.904A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 247 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 247' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.529A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.679A pdb=" N TYR A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 5.061A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.895A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.310A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.616A pdb=" N ALA A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 708 Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.863A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.532A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 Proline residue: A 868 - end of helix removed outlier: 4.885A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.306A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.595A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 32 through 96 removed outlier: 3.610A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.768A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.746A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.574A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.854A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.657A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 32 through 81 removed outlier: 4.373A pdb=" N LYS D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 4.344A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 128 through 148 Processing helix chain 'E' and resid 263 through 274 removed outlier: 4.675A pdb=" N ALA E 267 " --> pdb=" O SER E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 327 through 329 No H-bonds generated for 'chain 'E' and resid 327 through 329' Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 432 Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 504 through 508 removed outlier: 4.048A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 525 removed outlier: 3.658A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 567 removed outlier: 4.326A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 Processing helix chain 'F' and resid 27 through 34 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 128 through 148 Processing helix chain 'F' and resid 263 through 274 removed outlier: 4.676A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 Processing helix chain 'F' and resid 312 through 324 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 376 through 378 No H-bonds generated for 'chain 'F' and resid 376 through 378' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 432 Processing helix chain 'F' and resid 446 through 454 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 504 through 508 removed outlier: 4.049A pdb=" N LYS F 508 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.658A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 567 removed outlier: 4.326A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 584 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.036A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'A' and resid 99 through 105 Processing sheet with id= E, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.644A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= G, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= H, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.469A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= J, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= K, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.510A pdb=" N ILE B 132 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.452A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 224 through 227 removed outlier: 4.338A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 277 through 280 removed outlier: 6.562A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR E 359 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 471 through 474 removed outlier: 6.598A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 152 through 157 removed outlier: 7.341A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= S, first strand: chain 'F' and resid 224 through 227 removed outlier: 4.337A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.561A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 374 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR F 307 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR F 359 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 471 through 474 removed outlier: 6.598A pdb=" N ILE F 572 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N MET F 474 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS F 574 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 152 through 157 removed outlier: 7.342A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 8.55 Time building geometry restraints manager: 9.07 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: 5398 1.33 - 1.45: 4823 1.45 - 1.57: 11962 1.57 - 1.69: 219 1.69 - 1.81: 220 Bond restraints: 22622 Sorted by residual: bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 22617 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.26: 761 105.26 - 112.89: 12455 112.89 - 120.52: 9886 120.52 - 128.14: 7777 128.14 - 135.77: 243 Bond angle restraints: 31122 Sorted by residual: angle pdb=" N ILE A 856 " pdb=" CA ILE A 856 " pdb=" C ILE A 856 " ideal model delta sigma weight residual 112.96 105.97 6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" O3' C P 25 " pdb=" C3' C P 25 " pdb=" C2' C P 25 " ideal model delta sigma weight residual 113.70 119.77 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 118.59 -8.78 2.21e+00 2.05e-01 1.58e+01 angle pdb=" C PHE F 499 " pdb=" N LEU F 500 " pdb=" CA LEU F 500 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 ... (remaining 31117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 13202 33.68 - 67.37: 449 67.37 - 101.05: 64 101.05 - 134.74: 18 134.74 - 168.42: 2 Dihedral angle restraints: 13735 sinusoidal: 6176 harmonic: 7559 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual -180.00 -107.57 -72.43 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA PRO E 514 " pdb=" C PRO E 514 " pdb=" N TYR E 515 " pdb=" CA TYR E 515 " ideal model delta harmonic sigma weight residual 180.00 134.35 45.65 0 5.00e+00 4.00e-02 8.34e+01 dihedral pdb=" CA PRO F 514 " pdb=" C PRO F 514 " pdb=" N TYR F 515 " pdb=" CA TYR F 515 " ideal model delta harmonic sigma weight residual 180.00 134.37 45.63 0 5.00e+00 4.00e-02 8.33e+01 ... (remaining 13732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.029: 3614 1.029 - 2.059: 0 2.059 - 3.088: 0 3.088 - 4.118: 0 4.118 - 5.147: 2 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.72 -5.15 2.00e-01 2.50e+01 6.62e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.54 5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" C15 1N7 A1005 " pdb=" C14 1N7 A1005 " pdb=" C16 1N7 A1005 " pdb=" C2 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.47 -2.88 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 3613 not shown) Planarity restraints: 3649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 183 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 927 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 94 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.028 5.00e-02 4.00e+02 ... (remaining 3646 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 39 2.27 - 2.93: 9654 2.93 - 3.59: 32445 3.59 - 4.24: 51821 4.24 - 4.90: 84732 Nonbonded interactions: 178691 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.614 2.170 nonbonded pdb=" O1B ADP A1004 " pdb=" O2A ADP A1004 " model vdw 1.807 3.040 nonbonded pdb=" O3B ADP F1003 " pdb="MG MG F1004 " model vdw 1.841 2.170 nonbonded pdb=" O3B ADP E 704 " pdb="MG MG E 705 " model vdw 1.841 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb=" O2A ADP A1004 " model vdw 1.845 3.040 ... (remaining 178686 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 'B' and resid 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 590 or resid 701 through 706)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 8.090 Check model and map are aligned: 0.350 Set scattering table: 0.250 Process input model: 66.960 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.009 0.164 22622 Z= 0.538 Angle : 0.782 11.165 31122 Z= 0.408 Chirality : 0.131 5.147 3616 Planarity : 0.005 0.104 3649 Dihedral : 17.252 168.423 8861 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.93 % Favored : 92.76 % Rotamer: Outliers : 9.40 % Allowed : 10.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -1.73 (0.16), residues: 2541 helix: -0.55 (0.16), residues: 1012 sheet: -1.05 (0.29), residues: 331 loop : -1.64 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 182 HIS 0.008 0.001 HIS F 290 PHE 0.021 0.002 PHE A 920 TYR 0.023 0.002 TYR A 748 ARG 0.005 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 311 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 209 outliers final: 74 residues processed: 507 average time/residue: 0.3587 time to fit residues: 282.2999 Evaluate side-chains 275 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 201 time to evaluate : 2.240 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 74 outliers final: 1 residues processed: 74 average time/residue: 0.2220 time to fit residues: 33.6906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 236 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 703 ASN A 722 ASN A 724 GLN D 65 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 179 ASN E 194 GLN E 548 GLN F 194 GLN F 265 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22622 Z= 0.200 Angle : 0.604 9.245 31122 Z= 0.302 Chirality : 0.041 0.277 3616 Planarity : 0.004 0.088 3649 Dihedral : 13.921 169.620 4192 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.67 % Favored : 94.02 % Rotamer: Outliers : 3.06 % Allowed : 17.41 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.27 (0.16), residues: 2541 helix: 0.03 (0.17), residues: 1005 sheet: -0.77 (0.29), residues: 310 loop : -1.59 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 506 HIS 0.007 0.001 HIS E 290 PHE 0.031 0.001 PHE E 475 TYR 0.023 0.001 TYR F 324 ARG 0.009 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 244 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 33 residues processed: 300 average time/residue: 0.3355 time to fit residues: 157.9150 Evaluate side-chains 226 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 2.512 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.1994 time to fit residues: 15.5966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 50.0000 chunk 234 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN B 179 ASN D 158 GLN E 46 ASN E 194 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN F 537 GLN F 548 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22622 Z= 0.390 Angle : 0.654 9.534 31122 Z= 0.334 Chirality : 0.044 0.245 3616 Planarity : 0.004 0.096 3649 Dihedral : 13.416 158.910 4192 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.40 % Favored : 92.29 % Rotamer: Outliers : 3.55 % Allowed : 19.12 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.35 (0.16), residues: 2541 helix: -0.03 (0.16), residues: 1002 sheet: -0.89 (0.28), residues: 327 loop : -1.62 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 182 HIS 0.009 0.001 HIS E 290 PHE 0.019 0.002 PHE A 70 TYR 0.022 0.002 TYR A 748 ARG 0.007 0.001 ARG F 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 209 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 43 residues processed: 274 average time/residue: 0.3384 time to fit residues: 146.6128 Evaluate side-chains 234 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 2.312 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 43 outliers final: 1 residues processed: 43 average time/residue: 0.1967 time to fit residues: 19.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 724 GLN D 179 ASN E 194 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN F 265 ASN F 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22622 Z= 0.324 Angle : 0.608 10.392 31122 Z= 0.308 Chirality : 0.042 0.234 3616 Planarity : 0.004 0.093 3649 Dihedral : 13.113 133.702 4192 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.41 % Favored : 93.27 % Rotamer: Outliers : 3.33 % Allowed : 20.11 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.26 (0.17), residues: 2541 helix: 0.06 (0.16), residues: 1012 sheet: -0.86 (0.29), residues: 329 loop : -1.59 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 182 HIS 0.007 0.001 HIS E 290 PHE 0.026 0.002 PHE E 475 TYR 0.018 0.002 TYR A 453 ARG 0.006 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 200 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 37 residues processed: 259 average time/residue: 0.3233 time to fit residues: 134.5485 Evaluate side-chains 223 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 2.295 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.1956 time to fit residues: 16.8629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 214 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN F 268 ASN F 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22622 Z= 0.193 Angle : 0.554 11.725 31122 Z= 0.278 Chirality : 0.039 0.220 3616 Planarity : 0.004 0.087 3649 Dihedral : 12.782 124.979 4192 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.82 % Favored : 93.86 % Rotamer: Outliers : 1.71 % Allowed : 21.37 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.05 (0.17), residues: 2541 helix: 0.29 (0.17), residues: 999 sheet: -0.80 (0.29), residues: 325 loop : -1.50 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 182 HIS 0.005 0.001 HIS E 290 PHE 0.017 0.001 PHE A 652 TYR 0.016 0.001 TYR B 138 ARG 0.006 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 238 average time/residue: 0.3571 time to fit residues: 134.6339 Evaluate side-chains 203 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 2.376 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.2043 time to fit residues: 10.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 251 optimal weight: 0.0770 chunk 208 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 388 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 ASN E 548 GLN F 395 HIS F 537 GLN F 548 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22622 Z= 0.191 Angle : 0.548 12.207 31122 Z= 0.274 Chirality : 0.039 0.219 3616 Planarity : 0.004 0.086 3649 Dihedral : 12.585 124.841 4192 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.71 % Favored : 93.98 % Rotamer: Outliers : 1.57 % Allowed : 21.64 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2541 helix: 0.40 (0.17), residues: 995 sheet: -0.73 (0.29), residues: 327 loop : -1.45 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.004 0.001 HIS E 290 PHE 0.018 0.001 PHE E 475 TYR 0.019 0.001 TYR E 515 ARG 0.006 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 227 average time/residue: 0.3633 time to fit residues: 128.2240 Evaluate side-chains 200 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 2.246 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.2210 time to fit residues: 9.8245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.0770 chunk 183 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS F 548 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22622 Z= 0.190 Angle : 0.550 12.025 31122 Z= 0.273 Chirality : 0.039 0.214 3616 Planarity : 0.004 0.147 3649 Dihedral : 12.467 124.824 4192 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 1.30 % Allowed : 22.09 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: -0.87 (0.17), residues: 2541 helix: 0.43 (0.17), residues: 994 sheet: -0.64 (0.29), residues: 327 loop : -1.40 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 652 TYR 0.024 0.001 TYR F 324 ARG 0.013 0.000 ARG F 497 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 216 average time/residue: 0.3683 time to fit residues: 125.0859 Evaluate side-chains 195 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 2.675 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.2646 time to fit residues: 9.2137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN F 46 ASN ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22622 Z= 0.219 Angle : 0.572 12.588 31122 Z= 0.283 Chirality : 0.040 0.215 3616 Planarity : 0.004 0.099 3649 Dihedral : 12.393 124.852 4192 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.86 % Favored : 93.82 % Rotamer: Outliers : 0.90 % Allowed : 22.49 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: -0.86 (0.17), residues: 2541 helix: 0.44 (0.17), residues: 997 sheet: -0.62 (0.29), residues: 327 loop : -1.39 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 182 HIS 0.004 0.001 HIS E 290 PHE 0.015 0.001 PHE E 475 TYR 0.022 0.001 TYR B 22 ARG 0.007 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 207 average time/residue: 0.3511 time to fit residues: 113.9848 Evaluate side-chains 189 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 2.321 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2040 time to fit residues: 6.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 101 optimal weight: 0.2980 chunk 183 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 220 optimal weight: 0.0770 chunk 232 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 534 ASN A 790 ASN F 230 HIS F 268 ASN F 548 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22622 Z= 0.159 Angle : 0.556 12.575 31122 Z= 0.274 Chirality : 0.039 0.206 3616 Planarity : 0.004 0.095 3649 Dihedral : 12.274 124.802 4192 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.16 % Favored : 94.53 % Rotamer: Outliers : 0.40 % Allowed : 22.90 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: -0.76 (0.17), residues: 2541 helix: 0.50 (0.17), residues: 1000 sheet: -0.54 (0.29), residues: 327 loop : -1.33 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 652 TYR 0.032 0.001 TYR B 22 ARG 0.008 0.000 ARG F 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 196 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 199 average time/residue: 0.3395 time to fit residues: 108.3126 Evaluate side-chains 185 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 2.452 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2382 time to fit residues: 5.6842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 259 optimal weight: 20.0000 chunk 238 optimal weight: 40.0000 chunk 206 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 22622 Z= 0.504 Angle : 0.726 12.299 31122 Z= 0.366 Chirality : 0.046 0.239 3616 Planarity : 0.005 0.096 3649 Dihedral : 12.549 125.005 4192 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.19 % Favored : 91.50 % Rotamer: Outliers : 0.49 % Allowed : 23.12 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: -1.23 (0.17), residues: 2541 helix: 0.04 (0.17), residues: 1011 sheet: -0.79 (0.29), residues: 334 loop : -1.54 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 182 HIS 0.008 0.001 HIS A 75 PHE 0.021 0.002 PHE A 340 TYR 0.035 0.002 TYR B 22 ARG 0.008 0.001 ARG F 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 197 average time/residue: 0.3706 time to fit residues: 119.3145 Evaluate side-chains 187 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 2.387 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2409 time to fit residues: 6.9446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.9990 chunk 219 optimal weight: 50.0000 chunk 63 optimal weight: 0.5980 chunk 190 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 212 optimal weight: 30.0000 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104747 restraints weight = 32105.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103964 restraints weight = 33806.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104939 restraints weight = 35569.461| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22622 Z= 0.173 Angle : 0.597 12.540 31122 Z= 0.297 Chirality : 0.040 0.271 3616 Planarity : 0.004 0.084 3649 Dihedral : 12.377 125.168 4192 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.08 % Favored : 94.61 % Rotamer: Outliers : 0.22 % Allowed : 23.39 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2541 helix: 0.29 (0.17), residues: 1009 sheet: -0.69 (0.29), residues: 329 loop : -1.34 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 182 HIS 0.004 0.001 HIS E 290 PHE 0.020 0.001 PHE F 357 TYR 0.059 0.001 TYR B 22 ARG 0.013 0.000 ARG F 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4217.91 seconds wall clock time: 78 minutes 43.38 seconds (4723.38 seconds total)