Starting phenix.real_space_refine (version: dev) on Thu Dec 15 06:12:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/12_2022/6why_21680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/12_2022/6why_21680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/12_2022/6why_21680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/12_2022/6why_21680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/12_2022/6why_21680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/12_2022/6why_21680_updated.pdb" } resolution = 4.03 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= 0.017 sd= 0.833 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2138 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B GLU 744": "OE1" <-> "OE2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 822": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D ARG 505": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D GLU 788": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22198 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 5608 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 33, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 785 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 14, 'TYR:plan': 3, 'ASN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 26, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 439 Chain: "B" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5424 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 26, 'TRANS': 732} Chain breaks: 5 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 734 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 27, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 404 Chain: "C" Number of atoms: 5608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 5608 Classifications: {'peptide': 790} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 33, 'TRANS': 756} Chain breaks: 4 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 785 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 14, 'TYR:plan': 3, 'ASN:plan1': 11, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 26, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 439 Chain: "D" Number of atoms: 5424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 5424 Classifications: {'peptide': 759} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 26, 'TRANS': 732} Chain breaks: 5 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 734 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 12, 'TYR:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 27, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 404 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.15, per 1000 atoms: 0.55 Number of scatterers: 22198 At special positions: 0 Unit cell: (141.11, 147.96, 182.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 126 16.00 O 4158 8.00 N 3626 7.00 C 14284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.05 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.01 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.04 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.05 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 903 " - " ASN B 542 " " NAG D 903 " - " ASN D 542 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.30 Conformation dependent library (CDL) restraints added in 3.9 seconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 30 sheets defined 38.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.748A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 4.719A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.528A pdb=" N VAL A 150 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 157 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.521A pdb=" N MET A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 removed outlier: 3.808A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG A 254 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.570A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 479 through 491 removed outlier: 4.208A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 543 through 546 removed outlier: 3.658A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 575 through 578 Proline residue: A 578 - end of helix No H-bonds generated for 'chain 'A' and resid 575 through 578' Processing helix chain 'A' and resid 581 through 603 removed outlier: 4.087A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.660A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 677 removed outlier: 4.011A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 659 " --> pdb=" O MET A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 693 No H-bonds generated for 'chain 'A' and resid 691 through 693' Processing helix chain 'A' and resid 711 through 714 No H-bonds generated for 'chain 'A' and resid 711 through 714' Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 735 through 743 removed outlier: 3.747A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 removed outlier: 4.899A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 802 removed outlier: 3.908A pdb=" N GLU A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 831 through 860 removed outlier: 5.453A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE A 838 " --> pdb=" O MET A 834 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 59 removed outlier: 4.644A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 106 through 119 removed outlier: 3.829A pdb=" N LEU B 112 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE B 114 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 117 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 179 through 188 Processing helix chain 'B' and resid 216 through 222 removed outlier: 4.623A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 247 removed outlier: 4.143A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 283 through 286 No H-bonds generated for 'chain 'B' and resid 283 through 286' Processing helix chain 'B' and resid 289 through 310 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 461 through 470 removed outlier: 4.700A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 517 through 522 removed outlier: 4.310A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 removed outlier: 4.495A pdb=" N PHE B 550 " --> pdb=" O PRO B 547 " (cutoff:3.500A) Proline residue: B 553 - end of helix Processing helix chain 'B' and resid 556 through 577 removed outlier: 3.507A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 613 removed outlier: 4.568A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 655 removed outlier: 3.504A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 690 through 696 removed outlier: 3.906A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 695 " --> pdb=" O THR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 708 removed outlier: 4.952A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 733 through 739 Processing helix chain 'B' and resid 771 through 783 removed outlier: 3.975A pdb=" N ARG B 774 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 776 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU B 781 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 817 through 843 removed outlier: 4.176A pdb=" N GLY B 820 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 834 " --> pdb=" O LEU B 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.748A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 removed outlier: 4.719A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.528A pdb=" N VAL C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 157 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 186 Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.521A pdb=" N MET C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 removed outlier: 3.809A pdb=" N ALA C 250 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ARG C 254 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 299 through 315 removed outlier: 3.569A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 479 through 491 removed outlier: 4.208A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 528 Processing helix chain 'C' and resid 543 through 546 removed outlier: 3.659A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 546' Processing helix chain 'C' and resid 575 through 578 Proline residue: C 578 - end of helix No H-bonds generated for 'chain 'C' and resid 575 through 578' Processing helix chain 'C' and resid 581 through 603 removed outlier: 4.087A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.660A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 677 removed outlier: 4.011A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 693 No H-bonds generated for 'chain 'C' and resid 691 through 693' Processing helix chain 'C' and resid 711 through 714 No H-bonds generated for 'chain 'C' and resid 711 through 714' Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 735 through 743 removed outlier: 3.748A pdb=" N ILE C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 761 removed outlier: 4.899A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 802 removed outlier: 3.908A pdb=" N GLU C 802 " --> pdb=" O LEU C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 811 Processing helix chain 'C' and resid 831 through 860 removed outlier: 5.454A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 59 removed outlier: 4.644A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 106 through 119 removed outlier: 3.829A pdb=" N LEU D 112 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE D 114 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 116 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 117 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 179 through 188 Processing helix chain 'D' and resid 216 through 222 removed outlier: 4.622A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 removed outlier: 4.143A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 283 through 286 No H-bonds generated for 'chain 'D' and resid 283 through 286' Processing helix chain 'D' and resid 289 through 310 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 461 through 470 removed outlier: 4.700A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 499 No H-bonds generated for 'chain 'D' and resid 496 through 499' Processing helix chain 'D' and resid 517 through 522 removed outlier: 4.311A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 removed outlier: 4.495A pdb=" N PHE D 550 " --> pdb=" O PRO D 547 " (cutoff:3.500A) Proline residue: D 553 - end of helix Processing helix chain 'D' and resid 556 through 577 removed outlier: 3.506A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 613 removed outlier: 4.567A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 655 removed outlier: 3.505A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D 653 " --> pdb=" O ASN D 649 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 690 through 696 removed outlier: 3.906A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE D 695 " --> pdb=" O THR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 removed outlier: 4.952A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 722 Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 771 through 783 removed outlier: 3.975A pdb=" N ARG D 774 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL D 776 " --> pdb=" O LYS D 773 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 781 " --> pdb=" O LEU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 817 through 843 removed outlier: 4.176A pdb=" N GLY D 820 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 834 " --> pdb=" O LEU D 831 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 32 removed outlier: 3.796A pdb=" N GLN A 61 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.866A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N PHE A 218 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 167 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 241 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A 168 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 267 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 242 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 269 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 371 through 373 Processing sheet with id= E, first strand: chain 'A' and resid 375 through 377 Processing sheet with id= F, first strand: chain 'A' and resid 421 through 423 Processing sheet with id= G, first strand: chain 'A' and resid 431 through 433 Processing sheet with id= H, first strand: chain 'A' and resid 508 through 511 Processing sheet with id= I, first strand: chain 'A' and resid 555 through 557 removed outlier: 4.446A pdb=" N LYS A 555 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 777 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 750 through 753 Processing sheet with id= K, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= L, first strand: chain 'B' and resid 202 through 204 removed outlier: 6.682A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 172 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 230 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 278 through 281 removed outlier: 6.934A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 417 through 420 Processing sheet with id= O, first strand: chain 'B' and resid 728 through 732 removed outlier: 3.867A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 27 through 32 removed outlier: 3.796A pdb=" N GLN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= R, first strand: chain 'C' and resid 215 through 218 removed outlier: 6.866A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N PHE C 218 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 167 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE C 241 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 168 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL C 267 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU C 242 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 269 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 371 through 373 Processing sheet with id= T, first strand: chain 'C' and resid 375 through 377 Processing sheet with id= U, first strand: chain 'C' and resid 421 through 423 Processing sheet with id= V, first strand: chain 'C' and resid 431 through 433 Processing sheet with id= W, first strand: chain 'C' and resid 508 through 511 Processing sheet with id= X, first strand: chain 'C' and resid 555 through 557 removed outlier: 4.446A pdb=" N LYS C 555 " --> pdb=" O PHE C 779 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 777 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 750 through 753 Processing sheet with id= Z, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'D' and resid 202 through 204 removed outlier: 6.682A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 172 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 278 through 281 removed outlier: 6.935A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 417 through 420 Processing sheet with id= AD, first strand: chain 'D' and resid 728 through 732 removed outlier: 3.868A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.30 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3670 1.31 - 1.44: 6017 1.44 - 1.57: 12767 1.57 - 1.70: 0 1.70 - 1.83: 214 Bond restraints: 22668 Sorted by residual: bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.472 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.472 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" ND2 QGM A1001 " pdb=" CAR QGM A1001 " ideal model delta sigma weight residual 1.354 1.454 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" ND2 QGM C1001 " pdb=" CAR QGM C1001 " ideal model delta sigma weight residual 1.354 1.454 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" CAR QGM A1001 " pdb=" NAN QGM A1001 " ideal model delta sigma weight residual 1.376 1.455 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 22663 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.91: 525 105.91 - 112.95: 12682 112.95 - 119.98: 7557 119.98 - 127.01: 10025 127.01 - 134.05: 273 Bond angle restraints: 31062 Sorted by residual: angle pdb=" N GLN C 791 " pdb=" CA GLN C 791 " pdb=" C GLN C 791 " ideal model delta sigma weight residual 111.28 104.55 6.73 1.09e+00 8.42e-01 3.81e+01 angle pdb=" N GLN A 791 " pdb=" CA GLN A 791 " pdb=" C GLN A 791 " ideal model delta sigma weight residual 111.28 104.58 6.70 1.09e+00 8.42e-01 3.77e+01 angle pdb=" C ASP D 661 " pdb=" N GLN D 662 " pdb=" CA GLN D 662 " ideal model delta sigma weight residual 121.90 114.25 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C ASP B 661 " pdb=" N GLN B 662 " pdb=" CA GLN B 662 " ideal model delta sigma weight residual 121.90 114.26 7.64 1.26e+00 6.30e-01 3.68e+01 angle pdb=" O LYS C 790 " pdb=" C LYS C 790 " pdb=" N GLN C 791 " ideal model delta sigma weight residual 122.08 128.20 -6.12 1.07e+00 8.73e-01 3.27e+01 ... (remaining 31057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.70: 12229 20.70 - 41.39: 796 41.39 - 62.09: 143 62.09 - 82.78: 22 82.78 - 103.48: 8 Dihedral angle restraints: 13198 sinusoidal: 4244 harmonic: 8954 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 329 " pdb=" CB CYS C 329 " ideal model delta sinusoidal sigma weight residual 93.00 30.94 62.06 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 329 " pdb=" CB CYS A 329 " ideal model delta sinusoidal sigma weight residual 93.00 30.95 62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS D 429 " pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual 93.00 150.05 -57.05 1 1.00e+01 1.00e-02 4.38e+01 ... (remaining 13195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.303: 3792 0.303 - 0.606: 2 0.606 - 0.909: 0 0.909 - 1.211: 0 1.211 - 1.514: 2 Chirality restraints: 3796 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.73e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.73e+03 chirality pdb=" CG QGM A1001 " pdb=" CB QGM A1001 " pdb=" CD1 QGM A1001 " pdb=" ND2 QGM A1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 3793 not shown) Planarity restraints: 3934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 792 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C GLN A 792 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 792 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 793 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 792 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C GLN C 792 " 0.041 2.00e-02 2.50e+03 pdb=" O GLN C 792 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL C 793 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 791 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C GLN A 791 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN A 791 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN A 792 " 0.012 2.00e-02 2.50e+03 ... (remaining 3931 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1151 2.70 - 3.25: 24871 3.25 - 3.80: 34183 3.80 - 4.35: 40221 4.35 - 4.90: 63591 Nonbonded interactions: 164017 Sorted by model distance: nonbonded pdb=" O ASP C 248 " pdb=" OG1 THR C 251 " model vdw 2.150 2.440 nonbonded pdb=" O ASP A 248 " pdb=" OG1 THR A 251 " model vdw 2.150 2.440 nonbonded pdb=" OG1 THR C 446 " pdb=" OD1 ASP C 450 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR A 446 " pdb=" OD1 ASP A 450 " model vdw 2.155 2.440 nonbonded pdb=" O LEU A 487 " pdb=" OG1 THR A 490 " model vdw 2.158 2.440 ... (remaining 164012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 Cl 4 4.86 5 C 14284 2.51 5 N 3626 2.21 5 O 4158 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 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 5.660 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.180 Process input model: 58.020 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 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 0.125 22668 Z= 0.380 Angle : 0.830 14.242 31062 Z= 0.477 Chirality : 0.059 1.514 3796 Planarity : 0.005 0.047 3930 Dihedral : 14.572 103.476 7352 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.12 (0.12), residues: 3054 helix: -2.89 (0.12), residues: 1128 sheet: -3.46 (0.21), residues: 334 loop : -3.86 (0.13), residues: 1592 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 299 time to evaluate : 2.669 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: 36 outliers final: 17 residues processed: 324 average time/residue: 0.2684 time to fit residues: 145.3888 Evaluate side-chains 230 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 213 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2010 time to fit residues: 10.0753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 260 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 GLN ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN A 498 HIS B 110 GLN B 159 ASN B 621 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 498 HIS D 110 GLN D 621 GLN D 672 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 22668 Z= 0.294 Angle : 0.702 12.693 31062 Z= 0.371 Chirality : 0.046 0.182 3796 Planarity : 0.005 0.041 3930 Dihedral : 8.357 103.481 3254 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.96 (0.13), residues: 3054 helix: -1.68 (0.14), residues: 1140 sheet: -3.09 (0.23), residues: 320 loop : -3.35 (0.14), residues: 1594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 286 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 289 average time/residue: 0.2648 time to fit residues: 130.1761 Evaluate side-chains 221 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1817 time to fit residues: 3.7506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 155 optimal weight: 30.0000 chunk 86 optimal weight: 0.1980 chunk 232 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 280 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 249 optimal weight: 0.0970 chunk 277 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 134 HIS A 146 HIS A 297 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 592 HIS B 672 GLN B 840 HIS C 38 HIS C 73 GLN C 134 HIS C 146 HIS C 297 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 HIS C 542 ASN D 840 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 22668 Z= 0.174 Angle : 0.610 10.192 31062 Z= 0.324 Chirality : 0.044 0.197 3796 Planarity : 0.004 0.050 3930 Dihedral : 7.985 103.569 3254 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.11 (0.14), residues: 3054 helix: -0.87 (0.15), residues: 1166 sheet: -2.49 (0.24), residues: 362 loop : -2.99 (0.14), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 308 average time/residue: 0.2609 time to fit residues: 137.2013 Evaluate side-chains 236 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 2.544 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1802 time to fit residues: 3.7266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 276 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 281 optimal weight: 0.0870 chunk 297 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS C 38 HIS ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 592 HIS ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 22668 Z= 0.186 Angle : 0.611 8.639 31062 Z= 0.321 Chirality : 0.044 0.198 3796 Planarity : 0.004 0.046 3930 Dihedral : 7.827 103.361 3254 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.82 (0.14), residues: 3054 helix: -0.61 (0.15), residues: 1170 sheet: -2.37 (0.25), residues: 358 loop : -2.83 (0.14), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 305 average time/residue: 0.2670 time to fit residues: 138.7606 Evaluate side-chains 236 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 2.550 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1887 time to fit residues: 3.6300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 247 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 254 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 152 optimal weight: 2.9990 chunk 267 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22668 Z= 0.176 Angle : 0.603 10.894 31062 Z= 0.315 Chirality : 0.044 0.199 3796 Planarity : 0.004 0.046 3930 Dihedral : 7.721 103.491 3254 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.45 (0.15), residues: 3054 helix: -0.30 (0.15), residues: 1162 sheet: -2.14 (0.26), residues: 340 loop : -2.62 (0.15), residues: 1552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2714 time to fit residues: 145.1414 Evaluate side-chains 238 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 100 optimal weight: 8.9990 chunk 268 optimal weight: 0.3980 chunk 58 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 22668 Z= 0.250 Angle : 0.650 11.632 31062 Z= 0.340 Chirality : 0.045 0.192 3796 Planarity : 0.004 0.044 3930 Dihedral : 7.818 103.381 3254 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.42 (0.15), residues: 3054 helix: -0.31 (0.15), residues: 1154 sheet: -2.13 (0.25), residues: 376 loop : -2.56 (0.15), residues: 1524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.718 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: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2761 time to fit residues: 141.6389 Evaluate side-chains 226 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.548 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 287 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 296 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 291 GLN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 22668 Z= 0.269 Angle : 0.663 10.123 31062 Z= 0.347 Chirality : 0.045 0.190 3796 Planarity : 0.004 0.046 3930 Dihedral : 7.900 103.630 3254 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.44 (0.15), residues: 3054 helix: -0.33 (0.15), residues: 1154 sheet: -2.19 (0.24), residues: 382 loop : -2.53 (0.15), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2653 time to fit residues: 138.1551 Evaluate side-chains 230 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 188 optimal weight: 30.0000 chunk 202 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 22668 Z= 0.246 Angle : 0.656 9.619 31062 Z= 0.342 Chirality : 0.045 0.188 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.862 103.662 3254 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.44 (0.15), residues: 3054 helix: -0.39 (0.15), residues: 1194 sheet: -2.21 (0.25), residues: 362 loop : -2.53 (0.15), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 2.541 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: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2639 time to fit residues: 136.4778 Evaluate side-chains 228 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 270 optimal weight: 0.8980 chunk 284 optimal weight: 4.9990 chunk 259 optimal weight: 20.0000 chunk 276 optimal weight: 8.9990 chunk 166 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 275 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 22668 Z= 0.208 Angle : 0.637 9.391 31062 Z= 0.332 Chirality : 0.045 0.193 3796 Planarity : 0.004 0.043 3930 Dihedral : 7.783 103.667 3254 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.27 (0.15), residues: 3054 helix: -0.26 (0.15), residues: 1182 sheet: -1.97 (0.26), residues: 340 loop : -2.46 (0.15), residues: 1532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 2.709 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: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2800 time to fit residues: 142.5173 Evaluate side-chains 235 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 181 optimal weight: 0.0770 chunk 292 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 282 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 70 ASN ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22668 Z= 0.168 Angle : 0.615 9.190 31062 Z= 0.317 Chirality : 0.044 0.201 3796 Planarity : 0.004 0.044 3930 Dihedral : 7.600 103.599 3254 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.03 (0.15), residues: 3054 helix: -0.04 (0.16), residues: 1184 sheet: -1.85 (0.27), residues: 334 loop : -2.34 (0.15), residues: 1536 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.2604 time to fit residues: 138.7811 Evaluate side-chains 239 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 194 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.089381 restraints weight = 90940.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.089631 restraints weight = 59786.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.089907 restraints weight = 65869.894| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 22668 Z= 0.246 Angle : 0.646 9.157 31062 Z= 0.337 Chirality : 0.045 0.190 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.693 103.439 3254 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.10 (0.15), residues: 3054 helix: -0.08 (0.16), residues: 1150 sheet: -2.17 (0.26), residues: 350 loop : -2.26 (0.15), residues: 1554 =============================================================================== Job complete usr+sys time: 3587.09 seconds wall clock time: 66 minutes 25.85 seconds (3985.85 seconds total)