Starting phenix.real_space_refine on Mon Feb 19 10:06:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/02_2024/6why_21680_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/02_2024/6why_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_21680/02_2024/6why_21680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/02_2024/6why_21680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/02_2024/6why_21680_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6why_21680/02_2024/6why_21680_updated.pdb" } resolution = 4.03 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= 0.017 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 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. 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-5238/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.78, per 1000 atoms: 0.53 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: 8.66 Conformation dependent library (CDL) restraints added in 4.1 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: 5.11 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: 7.33 Time building geometry restraints manager: 9.35 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 - 21.45: 12358 21.45 - 42.90: 744 42.90 - 64.35: 142 64.35 - 85.80: 52 85.80 - 107.26: 24 Dihedral angle restraints: 13320 sinusoidal: 4366 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 13317 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 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 4.910 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 57.950 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.180 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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= 0.383 Angle : 0.834 14.242 31062 Z= 0.477 Chirality : 0.059 1.514 3796 Planarity : 0.005 0.047 3930 Dihedral : 16.278 107.256 7474 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 1.71 % Allowed : 8.44 % Favored : 89.86 % Cbeta Deviations : 0.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 789 HIS 0.007 0.002 HIS A 162 PHE 0.015 0.002 PHE C 630 TYR 0.024 0.002 TYR A 128 ARG 0.004 0.001 ARG A 380 *********************** 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 : 2.479 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: A 154 MET cc_start: 0.6381 (tpp) cc_final: 0.5975 (tpt) REVERT: A 597 MET cc_start: 0.7153 (ttt) cc_final: 0.6549 (ttt) REVERT: B 366 LEU cc_start: 0.5065 (tp) cc_final: 0.4855 (tp) REVERT: B 426 SER cc_start: 0.4249 (OUTLIER) cc_final: 0.4007 (m) REVERT: C 154 MET cc_start: 0.5906 (tpp) cc_final: 0.4804 (tpt) REVERT: C 486 LYS cc_start: 0.8291 (tmtt) cc_final: 0.8080 (tptp) REVERT: D 37 ILE cc_start: 0.6326 (mp) cc_final: 0.6001 (mt) REVERT: D 188 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7472 (t) REVERT: D 258 VAL cc_start: 0.6875 (m) cc_final: 0.6573 (m) REVERT: D 426 SER cc_start: 0.5455 (OUTLIER) cc_final: 0.4872 (m) REVERT: D 809 MET cc_start: 0.8685 (tmm) cc_final: 0.8421 (tmm) outliers start: 36 outliers final: 17 residues processed: 324 average time/residue: 0.2727 time to fit residues: 148.1771 Evaluate side-chains 234 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 2.581 ------------------------------------------------------------------------------- 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: 50.0000 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 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: 3.9990 ------------------------------------------------------------------------------- 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 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 HIS A 592 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 426 GLN C 498 HIS C 592 HIS D 110 GLN D 672 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22668 Z= 0.284 Angle : 0.713 11.533 31062 Z= 0.369 Chirality : 0.047 0.261 3796 Planarity : 0.004 0.041 3930 Dihedral : 10.463 87.905 3376 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.14 % Allowed : 6.49 % Favored : 93.36 % Cbeta Deviations : 0.00 % 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: -3.98 (0.13), residues: 3054 helix: -1.68 (0.14), residues: 1146 sheet: -3.04 (0.23), residues: 312 loop : -3.39 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 789 HIS 0.007 0.001 HIS C 162 PHE 0.022 0.002 PHE A 805 TYR 0.019 0.001 TYR C 128 ARG 0.003 0.000 ARG A 692 *********************** 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 291 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 288 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6333 (tpp) cc_final: 0.5841 (tpt) REVERT: B 654 MET cc_start: 0.8013 (mtm) cc_final: 0.7790 (mtp) REVERT: B 837 ILE cc_start: 0.7644 (mm) cc_final: 0.7435 (mm) REVERT: C 846 VAL cc_start: 0.7738 (m) cc_final: 0.7463 (t) outliers start: 3 outliers final: 0 residues processed: 290 average time/residue: 0.2613 time to fit residues: 128.9433 Evaluate side-chains 220 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.352 ------------------------------------------------------------------------------- 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: 0.8980 chunk 232 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 280 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 277 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 542 ASN 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 621 GLN D 840 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22668 Z= 0.165 Angle : 0.617 8.442 31062 Z= 0.322 Chirality : 0.045 0.249 3796 Planarity : 0.004 0.048 3930 Dihedral : 8.712 86.456 3376 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Cbeta Deviations : 0.00 % 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: -3.00 (0.14), residues: 3054 helix: -0.78 (0.15), residues: 1168 sheet: -2.44 (0.24), residues: 362 loop : -2.93 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 584 HIS 0.007 0.001 HIS C 425 PHE 0.016 0.001 PHE B 144 TYR 0.015 0.001 TYR B 479 ARG 0.004 0.000 ARG B 742 *********************** 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 306 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 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: A 154 MET cc_start: 0.6127 (tpp) cc_final: 0.5721 (tpt) REVERT: A 522 MET cc_start: 0.5121 (ptm) cc_final: 0.4845 (ptm) REVERT: B 161 MET cc_start: 0.6834 (mtp) cc_final: 0.6048 (ttm) REVERT: B 654 MET cc_start: 0.7558 (mtm) cc_final: 0.7348 (mtp) REVERT: C 154 MET cc_start: 0.5707 (tpp) cc_final: 0.5082 (tpt) REVERT: C 846 VAL cc_start: 0.7817 (m) cc_final: 0.7598 (t) REVERT: D 462 ILE cc_start: 0.7150 (mm) cc_final: 0.6916 (mm) REVERT: D 645 SER cc_start: 0.7790 (t) cc_final: 0.7575 (t) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2646 time to fit residues: 138.5218 Evaluate side-chains 235 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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: 0.9990 chunk 145 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 188 optimal weight: 30.0000 chunk 281 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 80 optimal weight: 0.0020 overall best weight: 1.3994 ------------------------------------------------------------------------------- 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 426 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22668 Z= 0.170 Angle : 0.612 8.958 31062 Z= 0.317 Chirality : 0.044 0.273 3796 Planarity : 0.004 0.047 3930 Dihedral : 8.189 81.635 3376 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Cbeta Deviations : 0.00 % 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: -2.72 (0.14), residues: 3054 helix: -0.53 (0.15), residues: 1170 sheet: -2.25 (0.26), residues: 342 loop : -2.79 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 610 HIS 0.004 0.001 HIS C 425 PHE 0.023 0.001 PHE B 143 TYR 0.015 0.001 TYR C 128 ARG 0.005 0.000 ARG D 693 *********************** 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 308 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.559 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: A 154 MET cc_start: 0.6056 (tpp) cc_final: 0.5567 (tpt) REVERT: B 837 ILE cc_start: 0.7456 (mm) cc_final: 0.7237 (mm) REVERT: C 154 MET cc_start: 0.5843 (tpp) cc_final: 0.5380 (tpt) REVERT: C 846 VAL cc_start: 0.7742 (m) cc_final: 0.7470 (t) REVERT: D 37 ILE cc_start: 0.5745 (mt) cc_final: 0.5404 (mp) REVERT: D 462 ILE cc_start: 0.7133 (mm) cc_final: 0.6896 (mm) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2622 time to fit residues: 138.2633 Evaluate side-chains 240 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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: 0.7980 chunk 168 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 221 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 152 optimal weight: 1.9990 chunk 267 optimal weight: 0.0050 chunk 75 optimal weight: 20.0000 overall best weight: 1.9600 ------------------------------------------------------------------------------- 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** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2543 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= 0.180 Angle : 0.609 11.063 31062 Z= 0.317 Chirality : 0.044 0.223 3796 Planarity : 0.004 0.046 3930 Dihedral : 7.798 75.878 3376 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % 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: -0.27 (0.15), residues: 1162 sheet: -2.11 (0.25), residues: 360 loop : -2.61 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 584 HIS 0.004 0.001 HIS C 425 PHE 0.021 0.001 PHE B 653 TYR 0.016 0.001 TYR A 668 ARG 0.003 0.000 ARG D 693 *********************** 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 306 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 2.431 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: A 154 MET cc_start: 0.6012 (tpp) cc_final: 0.5560 (tpt) REVERT: B 498 ILE cc_start: 0.7702 (mm) cc_final: 0.7496 (mm) REVERT: B 829 MET cc_start: 0.6830 (mtp) cc_final: 0.6365 (mtp) REVERT: C 154 MET cc_start: 0.5836 (tpp) cc_final: 0.5381 (tpt) REVERT: D 37 ILE cc_start: 0.5438 (mt) cc_final: 0.5114 (mp) REVERT: D 654 MET cc_start: 0.7174 (mtp) cc_final: 0.6870 (mtp) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2615 time to fit residues: 137.8665 Evaluate side-chains 237 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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: 9.9990 chunk 268 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 174 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.6496 moved from start: 0.2645 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= 0.224 Angle : 0.631 9.219 31062 Z= 0.327 Chirality : 0.044 0.198 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.674 74.377 3376 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % 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: -2.38 (0.15), residues: 3054 helix: -0.31 (0.15), residues: 1184 sheet: -2.05 (0.25), residues: 368 loop : -2.56 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 584 HIS 0.004 0.001 HIS C 67 PHE 0.044 0.002 PHE B 653 TYR 0.017 0.001 TYR C 128 ARG 0.003 0.000 ARG D 693 *********************** 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 300 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.685 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: A 154 MET cc_start: 0.5975 (tpp) cc_final: 0.5527 (tpt) REVERT: B 498 ILE cc_start: 0.7703 (mm) cc_final: 0.7435 (mm) REVERT: B 654 MET cc_start: 0.7580 (mtp) cc_final: 0.7297 (mtp) REVERT: C 154 MET cc_start: 0.5871 (tpp) cc_final: 0.5418 (tpt) REVERT: D 37 ILE cc_start: 0.5673 (mt) cc_final: 0.5300 (mp) REVERT: D 462 ILE cc_start: 0.7120 (mm) cc_final: 0.6915 (mm) REVERT: D 837 ILE cc_start: 0.7809 (mm) cc_final: 0.7569 (mm) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2727 time to fit residues: 140.6270 Evaluate side-chains 232 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 2.546 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22668 Z= 0.224 Angle : 0.637 9.246 31062 Z= 0.330 Chirality : 0.044 0.224 3796 Planarity : 0.004 0.043 3930 Dihedral : 7.554 73.231 3376 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % 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: -2.21 (0.15), residues: 3054 helix: -0.12 (0.15), residues: 1158 sheet: -2.06 (0.25), residues: 368 loop : -2.45 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 629 HIS 0.004 0.001 HIS C 425 PHE 0.035 0.002 PHE B 653 TYR 0.021 0.001 TYR A 128 ARG 0.004 0.000 ARG C 651 *********************** 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 311 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.697 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: A 154 MET cc_start: 0.5916 (tpp) cc_final: 0.5557 (tpt) REVERT: B 142 MET cc_start: 0.6587 (pmm) cc_final: 0.6380 (pmm) REVERT: B 161 MET cc_start: 0.6613 (mtp) cc_final: 0.6046 (ttm) REVERT: B 285 TRP cc_start: 0.6461 (m100) cc_final: 0.5703 (m100) REVERT: B 739 MET cc_start: 0.6843 (mmm) cc_final: 0.6641 (tpp) REVERT: C 154 MET cc_start: 0.5733 (tpp) cc_final: 0.5357 (tpt) REVERT: D 37 ILE cc_start: 0.5587 (mt) cc_final: 0.5216 (mp) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2547 time to fit residues: 136.9064 Evaluate side-chains 233 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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: 10.0000 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 672 GLN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN D 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22668 Z= 0.309 Angle : 0.692 10.021 31062 Z= 0.361 Chirality : 0.046 0.165 3796 Planarity : 0.004 0.043 3930 Dihedral : 7.785 78.794 3376 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 0.05 % Allowed : 1.47 % Favored : 98.48 % Cbeta Deviations : 0.00 % 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: -0.34 (0.15), residues: 1166 sheet: -2.35 (0.25), residues: 356 loop : -2.48 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 789 HIS 0.010 0.002 HIS B 486 PHE 0.054 0.002 PHE B 653 TYR 0.024 0.002 TYR C 128 ARG 0.003 0.000 ARG B 682 *********************** 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 295 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 294 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6018 (tpp) cc_final: 0.5603 (tpt) REVERT: B 142 MET cc_start: 0.6793 (pmm) cc_final: 0.6512 (pmm) REVERT: B 285 TRP cc_start: 0.6574 (m100) cc_final: 0.5818 (m100) REVERT: C 154 MET cc_start: 0.5824 (tpp) cc_final: 0.5459 (tpt) REVERT: D 37 ILE cc_start: 0.5711 (mt) cc_final: 0.5362 (mp) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.2609 time to fit residues: 131.9420 Evaluate side-chains 222 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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: 20.0000 chunk 284 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 276 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 217 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 261 optimal weight: 0.0270 chunk 275 optimal weight: 5.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 70 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3177 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= 0.168 Angle : 0.631 9.532 31062 Z= 0.324 Chirality : 0.044 0.192 3796 Planarity : 0.004 0.042 3930 Dihedral : 7.288 72.510 3376 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.05 % Allowed : 0.57 % Favored : 99.38 % Cbeta Deviations : 0.00 % 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: -2.14 (0.15), residues: 3054 helix: -0.08 (0.15), residues: 1176 sheet: -2.18 (0.26), residues: 346 loop : -2.37 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 789 HIS 0.011 0.001 HIS D 486 PHE 0.036 0.001 PHE D 143 TYR 0.025 0.001 TYR C 282 ARG 0.003 0.000 ARG D 693 *********************** 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 309 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 VAL cc_start: 0.7843 (m) cc_final: 0.7495 (t) REVERT: B 59 PHE cc_start: 0.3796 (m-80) cc_final: 0.3481 (m-80) REVERT: B 285 TRP cc_start: 0.6403 (m100) cc_final: 0.5661 (m100) REVERT: C 154 MET cc_start: 0.5584 (tpp) cc_final: 0.5257 (tpt) REVERT: D 837 ILE cc_start: 0.7696 (mm) cc_final: 0.7494 (mm) outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2633 time to fit residues: 139.4354 Evaluate side-chains 241 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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: 0.0070 chunk 292 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 306 optimal weight: 0.9990 chunk 282 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22668 Z= 0.162 Angle : 0.610 8.626 31062 Z= 0.312 Chirality : 0.044 0.184 3796 Planarity : 0.004 0.042 3930 Dihedral : 6.873 71.115 3376 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % 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: -1.95 (0.15), residues: 3054 helix: 0.06 (0.16), residues: 1180 sheet: -1.75 (0.27), residues: 358 loop : -2.34 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 285 HIS 0.011 0.001 HIS D 486 PHE 0.034 0.001 PHE D 143 TYR 0.024 0.001 TYR C 282 ARG 0.003 0.000 ARG B 693 ********************** 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 310 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 846 VAL cc_start: 0.7804 (m) cc_final: 0.7369 (t) REVERT: B 59 PHE cc_start: 0.3953 (m-80) cc_final: 0.3679 (m-80) REVERT: B 161 MET cc_start: 0.6701 (mtp) cc_final: 0.5858 (ttm) REVERT: D 498 ILE cc_start: 0.7594 (mm) cc_final: 0.7366 (mm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2640 time to fit residues: 140.4189 Evaluate side-chains 241 residues out of total 2690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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: 8.9990 chunk 260 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 225 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 244 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 251 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 45 optimal weight: 20.0000 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN B 672 GLN B 694 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.111232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.092083 restraints weight = 86877.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.093176 restraints weight = 54145.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093548 restraints weight = 42732.204| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3525 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= 0.178 Angle : 0.607 9.115 31062 Z= 0.310 Chirality : 0.044 0.178 3796 Planarity : 0.004 0.042 3930 Dihedral : 6.776 72.544 3376 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.62 % Cbeta Deviations : 0.00 % 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: -1.86 (0.15), residues: 3054 helix: 0.15 (0.16), residues: 1170 sheet: -1.67 (0.28), residues: 332 loop : -2.30 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 285 HIS 0.010 0.001 HIS D 486 PHE 0.033 0.001 PHE D 143 TYR 0.020 0.001 TYR C 282 ARG 0.004 0.000 ARG B 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3822.15 seconds wall clock time: 70 minutes 57.87 seconds (4257.87 seconds total)