Starting phenix.real_space_refine on Wed Feb 21 18:22:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi0_21681/02_2024/6wi0_21681_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi0_21681/02_2024/6wi0_21681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi0_21681/02_2024/6wi0_21681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi0_21681/02_2024/6wi0_21681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi0_21681/02_2024/6wi0_21681_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wi0_21681/02_2024/6wi0_21681_updated.pdb" } resolution = 4.27 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= 0.014 sd= 0.788 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 9484 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 106 5.16 5 Cl 4 4.86 5 C 14200 2.51 5 N 3586 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 807": "OE1" <-> "OE2" Residue "C PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 543": "OE1" <-> "OE2" Residue "C TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 807": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21964 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5545 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 32, 'TRANS': 759} Chain breaks: 4 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 616 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 9, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 484 Chain: "B" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5356 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 26, 'TRANS': 737} Chain breaks: 4 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 868 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 20, 'TYR:plan': 9, 'ASN:plan1': 7, 'HIS:plan': 7, 'PHE:plan': 8, 'GLU:plan': 30, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 479 Chain: "C" Number of atoms: 5545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5545 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 32, 'TRANS': 759} Chain breaks: 4 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 616 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 1, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 9, 'PHE:plan': 2, 'GLU:plan': 38, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 484 Chain: "D" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5356 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 26, 'TRANS': 737} Chain breaks: 4 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 868 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 20, 'TYR:plan': 9, 'ASN:plan1': 7, 'HIS:plan': 7, 'PHE:plan': 8, 'GLU:plan': 30, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 479 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: 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: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "D" 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 Time building chain proxies: 12.11, per 1000 atoms: 0.55 Number of scatterers: 21964 At special positions: 0 Unit cell: (138.37, 154.81, 183.58, 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 106 16.00 O 4068 8.00 N 3586 7.00 C 14200 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=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 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=2.04 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=2.04 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 901 " - " ASN B 542 " " NAG D 901 " - " 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: 9.51 Conformation dependent library (CDL) restraints added in 4.3 seconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 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: 5816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 24 sheets defined 38.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.643A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 3.704A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.646A pdb=" N ALA A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 145 through 157 removed outlier: 4.002A pdb=" N VAL A 150 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 154 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET A 155 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.651A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 removed outlier: 4.326A pdb=" N ALA A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.508A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.506A pdb=" N GLN A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.180A pdb=" N SER A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 removed outlier: 3.988A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 3.832A 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 544 through 547 Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 581 through 603 removed outlier: 3.840A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.757A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 677 removed outlier: 4.453A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (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 709 through 716 removed outlier: 3.622A pdb=" N ARG A 715 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 727 removed outlier: 3.858A pdb=" N SER A 721 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 722 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 743 removed outlier: 4.328A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 removed outlier: 4.533A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 803 removed outlier: 3.951A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 831 through 860 removed outlier: 6.524A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE A 838 " --> pdb=" O MET A 834 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 4.027A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 179 through 192 removed outlier: 4.225A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 removed outlier: 4.384A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 247 removed outlier: 4.147A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 310 Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.950A pdb=" N LEU B 339 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.574A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 518 through 522 removed outlier: 4.440A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 518 through 522' Processing helix chain 'B' and resid 556 through 576 removed outlier: 3.662A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.930A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 655 removed outlier: 3.605A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 5.299A 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 709 removed outlier: 7.144A pdb=" N GLU B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.784A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.733A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 820 through 844 removed outlier: 4.358A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.644A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 3.704A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.647A pdb=" N ALA C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 145 through 157 removed outlier: 4.003A pdb=" N VAL C 150 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET C 154 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N MET C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.651A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 256 removed outlier: 4.326A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.508A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 298 through 314 removed outlier: 3.506A pdb=" N GLN C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 348 removed outlier: 4.179A pdb=" N SER C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.989A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 3.833A 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 544 through 547 Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 581 through 603 removed outlier: 3.839A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 removed outlier: 3.757A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 677 removed outlier: 4.452A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 663 " --> pdb=" O GLY C 659 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (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 709 through 716 removed outlier: 3.622A pdb=" N ARG C 715 " --> pdb=" O ILE C 712 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 716 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 727 removed outlier: 3.859A pdb=" N SER C 721 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR C 722 " --> pdb=" O GLU C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 743 removed outlier: 4.329A pdb=" N ILE C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN C 740 " --> pdb=" O ALA C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 760 removed outlier: 4.533A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 803 removed outlier: 3.950A pdb=" N SER C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 803 " --> pdb=" O LYS C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 811 Processing helix chain 'C' and resid 831 through 860 removed outlier: 6.525A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 839 " --> pdb=" O ALA C 835 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 removed outlier: 4.026A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 179 through 192 removed outlier: 4.225A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 4.385A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 removed outlier: 4.147A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 310 Processing helix chain 'D' and resid 333 through 339 removed outlier: 3.951A pdb=" N LEU D 339 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 removed outlier: 3.573A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 500 No H-bonds generated for 'chain 'D' and resid 498 through 500' Processing helix chain 'D' and resid 518 through 522 removed outlier: 4.440A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 518 through 522' Processing helix chain 'D' and resid 556 through 576 removed outlier: 3.663A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.931A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 655 removed outlier: 3.605A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 653 " --> pdb=" O ASN D 649 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 5.299A 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 709 removed outlier: 7.143A pdb=" N GLU D 701 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE D 709 " --> pdb=" O TYR D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 722 Processing helix chain 'D' and resid 733 through 742 removed outlier: 4.784A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 742 " --> pdb=" O TYR D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.733A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 820 through 844 removed outlier: 4.358A pdb=" N LEU D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 59 through 65 Processing sheet with id= B, first strand: chain 'A' and resid 241 through 243 removed outlier: 7.019A pdb=" N LYS A 211 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU A 165 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLU A 213 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 13.004A pdb=" N VAL A 167 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N VAL A 215 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.076A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 431 through 433 Processing sheet with id= E, first strand: chain 'A' and resid 533 through 536 removed outlier: 4.409A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 559 through 563 Processing sheet with id= G, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.805A pdb=" N VAL B 39 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE B 99 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 124 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 228 through 231 removed outlier: 6.315A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.940A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN B 368 " --> pdb=" O TRP B 373 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TRP B 373 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 417 through 420 Processing sheet with id= K, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.078A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 729 through 732 Processing sheet with id= M, first strand: chain 'C' and resid 59 through 65 Processing sheet with id= N, first strand: chain 'C' and resid 241 through 243 removed outlier: 7.018A pdb=" N LYS C 211 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N LEU C 165 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLU C 213 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 13.005A pdb=" N VAL C 167 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N VAL C 215 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.076A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 431 through 433 Processing sheet with id= Q, first strand: chain 'C' and resid 533 through 536 removed outlier: 4.408A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 559 through 563 Processing sheet with id= S, first strand: chain 'D' and resid 69 through 73 removed outlier: 3.806A pdb=" N VAL D 39 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE D 99 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 124 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 228 through 231 removed outlier: 6.315A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 278 through 281 removed outlier: 3.940A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN D 368 " --> pdb=" O TRP D 373 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TRP D 373 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 417 through 420 Processing sheet with id= W, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.077A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 729 through 732 806 hydrogen bonds defined for protein. 2190 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: 8.15 Time building geometry restraints manager: 10.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3564 1.31 - 1.44: 6012 1.44 - 1.57: 12684 1.57 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 22434 Sorted by residual: bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.473 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.473 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" ND2 QGM C1001 " pdb=" CAR QGM C1001 " ideal model delta sigma weight residual 1.354 1.448 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" ND2 QGM A1001 " pdb=" CAR QGM A1001 " ideal model delta sigma weight residual 1.354 1.448 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAR QGM A1001 " pdb=" NAN QGM A1001 " ideal model delta sigma weight residual 1.376 1.454 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 22429 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.66: 445 105.66 - 112.76: 12551 112.76 - 119.86: 6979 119.86 - 126.97: 10567 126.97 - 134.07: 258 Bond angle restraints: 30800 Sorted by residual: angle pdb=" N VAL D 576 " pdb=" CA VAL D 576 " pdb=" C VAL D 576 " ideal model delta sigma weight residual 113.39 105.61 7.78 1.47e+00 4.63e-01 2.80e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 113.39 105.61 7.78 1.47e+00 4.63e-01 2.80e+01 angle pdb=" CA QGM A1001 " pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 123.80 108.88 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" CA QGM C1001 " pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 123.80 108.88 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C ILE B 85 " pdb=" N CYS B 86 " pdb=" CA CYS B 86 " ideal model delta sigma weight residual 121.14 114.38 6.76 1.75e+00 3.27e-01 1.49e+01 ... (remaining 30795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 12192 19.80 - 39.60: 771 39.60 - 59.41: 137 59.41 - 79.21: 20 79.21 - 99.01: 12 Dihedral angle restraints: 13132 sinusoidal: 4132 harmonic: 9000 Sorted by residual: dihedral pdb=" CB CYS A 831 " pdb=" SG CYS A 831 " pdb=" SG CYS D 557 " pdb=" CB CYS D 557 " ideal model delta sinusoidal sigma weight residual 93.00 6.42 86.58 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS B 557 " pdb=" SG CYS B 557 " pdb=" SG CYS C 831 " pdb=" CB CYS C 831 " ideal model delta sinusoidal sigma weight residual 93.00 6.79 86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CA GLU D 412 " pdb=" C GLU D 412 " pdb=" N GLU D 413 " pdb=" CA GLU D 413 " ideal model delta harmonic sigma weight residual 180.00 135.06 44.94 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 13129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 3806 0.307 - 0.613: 2 0.613 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.533: 2 Chirality restraints: 3810 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 -0.87 -1.53 2.00e-02 2.50e+03 5.88e+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 -0.87 -1.53 2.00e-02 2.50e+03 5.87e+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 -2.85 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 3807 not shown) Planarity restraints: 3886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 104 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 104 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 258 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 259 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.026 5.00e-02 4.00e+02 ... (remaining 3883 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 803 2.69 - 3.24: 24612 3.24 - 3.79: 34068 3.79 - 4.35: 41764 4.35 - 4.90: 63376 Nonbonded interactions: 164623 Sorted by model distance: nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.134 2.440 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.134 2.440 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 122 " model vdw 2.151 2.440 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR A 122 " model vdw 2.152 2.440 nonbonded pdb=" OG SER C 762 " pdb=" O TYR C 816 " model vdw 2.167 2.440 ... (remaining 164618 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=0.50 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 5.230 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 61.480 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 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 : 0.005 0.126 22434 Z= 0.348 Angle : 0.774 14.922 30800 Z= 0.436 Chirality : 0.058 1.533 3810 Planarity : 0.004 0.054 3882 Dihedral : 13.977 99.011 7262 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.19 % Favored : 89.62 % Rotamer: Outliers : 0.60 % Allowed : 7.54 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.12), residues: 3072 helix: -2.57 (0.12), residues: 1112 sheet: -3.00 (0.23), residues: 350 loop : -3.43 (0.13), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 796 HIS 0.005 0.001 HIS C 162 PHE 0.012 0.002 PHE B 784 TYR 0.013 0.002 TYR A 713 ARG 0.005 0.000 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 259 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6009 (mtp) cc_final: 0.5589 (mtm) REVERT: B 176 PHE cc_start: 0.6067 (t80) cc_final: 0.5649 (t80) REVERT: B 515 ILE cc_start: 0.8929 (mt) cc_final: 0.8690 (tt) REVERT: C 154 MET cc_start: 0.6229 (mtp) cc_final: 0.5756 (mtm) REVERT: D 300 ILE cc_start: 0.6747 (tt) cc_final: 0.6540 (mt) outliers start: 12 outliers final: 4 residues processed: 267 average time/residue: 0.2756 time to fit residues: 123.2535 Evaluate side-chains 190 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 50.0000 chunk 234 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 80 optimal weight: 0.0060 chunk 158 optimal weight: 40.0000 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 425 HIS A 426 GLN B 105 GLN B 127 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 341 ASN B 359 HIS B 615 ASN B 675 ASN B 817 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 177 GLN C 425 HIS C 426 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 192 ASN D 341 ASN D 359 HIS ** D 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22434 Z= 0.283 Angle : 0.666 8.649 30800 Z= 0.342 Chirality : 0.045 0.187 3810 Planarity : 0.004 0.058 3882 Dihedral : 8.491 92.275 3432 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.17 % Favored : 88.70 % Rotamer: Outliers : 0.30 % Allowed : 7.79 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.28 (0.14), residues: 3072 helix: -1.09 (0.14), residues: 1116 sheet: -2.59 (0.25), residues: 328 loop : -2.98 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 796 HIS 0.005 0.001 HIS C 162 PHE 0.012 0.002 PHE A 505 TYR 0.016 0.002 TYR C 713 ARG 0.004 0.000 ARG D 505 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7080 (mmm) cc_final: 0.6597 (mmt) REVERT: C 154 MET cc_start: 0.6092 (mtp) cc_final: 0.5820 (mtt) REVERT: C 261 MET cc_start: 0.7449 (mmm) cc_final: 0.7131 (mmt) outliers start: 6 outliers final: 3 residues processed: 241 average time/residue: 0.2692 time to fit residues: 110.5823 Evaluate side-chains 178 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN D 105 GLN D 118 GLN D 127 HIS ** D 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22434 Z= 0.355 Angle : 0.710 8.425 30800 Z= 0.368 Chirality : 0.046 0.234 3810 Planarity : 0.005 0.060 3882 Dihedral : 8.478 90.653 3432 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.27 % Favored : 87.60 % Rotamer: Outliers : 0.10 % Allowed : 7.24 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.87 (0.14), residues: 3072 helix: -0.70 (0.15), residues: 1120 sheet: -2.45 (0.24), residues: 360 loop : -2.74 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 796 HIS 0.006 0.001 HIS C 162 PHE 0.027 0.002 PHE D 842 TYR 0.019 0.002 TYR C 713 ARG 0.004 0.000 ARG D 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7074 (mmm) cc_final: 0.6666 (mmt) REVERT: B 176 PHE cc_start: 0.5940 (t80) cc_final: 0.5713 (t80) REVERT: C 154 MET cc_start: 0.6154 (mtp) cc_final: 0.5834 (mtt) REVERT: D 105 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5275 (mt0) REVERT: D 112 LEU cc_start: 0.7765 (pp) cc_final: 0.7513 (pp) outliers start: 2 outliers final: 0 residues processed: 218 average time/residue: 0.2591 time to fit residues: 97.0005 Evaluate side-chains 169 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 134 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 299 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 268 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN B 105 GLN B 153 GLN B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN D 615 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22434 Z= 0.156 Angle : 0.590 7.693 30800 Z= 0.298 Chirality : 0.043 0.200 3810 Planarity : 0.004 0.057 3882 Dihedral : 7.689 83.314 3432 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.52 % Favored : 92.35 % Rotamer: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.08 (0.15), residues: 3072 helix: 0.15 (0.16), residues: 1122 sheet: -2.49 (0.24), residues: 366 loop : -2.31 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 789 HIS 0.003 0.001 HIS C 146 PHE 0.032 0.001 PHE B 842 TYR 0.013 0.001 TYR D 287 ARG 0.007 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 254 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7119 (mmm) cc_final: 0.6756 (mmt) REVERT: B 105 GLN cc_start: 0.5346 (OUTLIER) cc_final: 0.4514 (mt0) REVERT: B 176 PHE cc_start: 0.5600 (t80) cc_final: 0.5365 (t80) REVERT: B 646 TYR cc_start: 0.8038 (t80) cc_final: 0.7786 (t80) REVERT: C 154 MET cc_start: 0.5917 (mtp) cc_final: 0.5623 (mtt) REVERT: D 112 LEU cc_start: 0.7764 (pp) cc_final: 0.7474 (pp) REVERT: D 646 TYR cc_start: 0.8143 (t80) cc_final: 0.7870 (t80) outliers start: 3 outliers final: 0 residues processed: 257 average time/residue: 0.2900 time to fit residues: 128.0261 Evaluate side-chains 185 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 255 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 492 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 22434 Z= 0.376 Angle : 0.729 12.420 30800 Z= 0.375 Chirality : 0.047 0.396 3810 Planarity : 0.005 0.061 3882 Dihedral : 8.031 85.938 3432 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.69 % Favored : 88.18 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 3072 helix: -0.15 (0.15), residues: 1112 sheet: -2.38 (0.24), residues: 382 loop : -2.33 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 796 HIS 0.006 0.001 HIS C 162 PHE 0.029 0.002 PHE C 550 TYR 0.021 0.002 TYR C 713 ARG 0.005 0.001 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.7637 (mmm) cc_final: 0.7312 (mmt) REVERT: A 723 MET cc_start: 0.6307 (mmm) cc_final: 0.5793 (mmm) REVERT: B 176 PHE cc_start: 0.6090 (t80) cc_final: 0.5827 (t80) REVERT: C 154 MET cc_start: 0.6177 (mtp) cc_final: 0.5760 (mtt) REVERT: D 112 LEU cc_start: 0.7899 (pp) cc_final: 0.7643 (pp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2607 time to fit residues: 100.2404 Evaluate side-chains 179 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 299 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 152 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN D 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22434 Z= 0.216 Angle : 0.621 10.924 30800 Z= 0.318 Chirality : 0.044 0.284 3810 Planarity : 0.004 0.059 3882 Dihedral : 7.648 82.272 3432 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.66 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -1.93 (0.15), residues: 3072 helix: 0.23 (0.16), residues: 1104 sheet: -2.31 (0.25), residues: 386 loop : -2.16 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 796 HIS 0.004 0.001 HIS C 162 PHE 0.035 0.001 PHE D 241 TYR 0.012 0.001 TYR C 713 ARG 0.004 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 LEU cc_start: 0.7639 (pp) cc_final: 0.7432 (pp) REVERT: B 142 MET cc_start: 0.4329 (mmm) cc_final: 0.3781 (mmp) REVERT: B 176 PHE cc_start: 0.5870 (t80) cc_final: 0.5662 (t80) REVERT: B 646 TYR cc_start: 0.8176 (t80) cc_final: 0.7969 (t80) REVERT: D 112 LEU cc_start: 0.7868 (pp) cc_final: 0.7490 (pp) REVERT: D 646 TYR cc_start: 0.8208 (t80) cc_final: 0.7984 (t80) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2894 time to fit residues: 111.5016 Evaluate side-chains 180 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22434 Z= 0.162 Angle : 0.584 10.609 30800 Z= 0.296 Chirality : 0.043 0.254 3810 Planarity : 0.004 0.060 3882 Dihedral : 7.061 80.232 3432 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: -1.55 (0.15), residues: 3072 helix: 0.65 (0.16), residues: 1106 sheet: -2.10 (0.24), residues: 424 loop : -2.01 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 796 HIS 0.002 0.000 HIS A 425 PHE 0.020 0.001 PHE D 241 TYR 0.014 0.001 TYR A 266 ARG 0.008 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 MET cc_start: 0.6212 (mmm) cc_final: 0.5715 (mmm) REVERT: B 176 PHE cc_start: 0.5913 (t80) cc_final: 0.5711 (t80) REVERT: B 646 TYR cc_start: 0.8054 (t80) cc_final: 0.7813 (t80) REVERT: D 112 LEU cc_start: 0.7767 (pp) cc_final: 0.7413 (pp) REVERT: D 142 MET cc_start: 0.4218 (mmm) cc_final: 0.3407 (mmp) REVERT: D 646 TYR cc_start: 0.7994 (t80) cc_final: 0.7759 (t80) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2571 time to fit residues: 105.9832 Evaluate side-chains 190 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.0670 chunk 119 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 0.0570 chunk 189 optimal weight: 9.9990 chunk 203 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 234 optimal weight: 8.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22434 Z= 0.137 Angle : 0.570 10.314 30800 Z= 0.284 Chirality : 0.042 0.226 3810 Planarity : 0.004 0.060 3882 Dihedral : 6.484 74.554 3432 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: -1.16 (0.16), residues: 3072 helix: 0.90 (0.16), residues: 1110 sheet: -1.81 (0.24), residues: 418 loop : -1.76 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 166 HIS 0.002 0.001 HIS A 425 PHE 0.030 0.001 PHE B 241 TYR 0.010 0.001 TYR A 266 ARG 0.010 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LEU cc_start: 0.7411 (pp) cc_final: 0.7183 (pp) REVERT: B 612 LEU cc_start: 0.7455 (tp) cc_final: 0.7235 (tp) REVERT: B 646 TYR cc_start: 0.7928 (t80) cc_final: 0.7679 (t80) REVERT: C 723 MET cc_start: 0.5112 (mmm) cc_final: 0.4664 (mmt) REVERT: D 112 LEU cc_start: 0.7640 (pp) cc_final: 0.7265 (pp) REVERT: D 142 MET cc_start: 0.3917 (mmm) cc_final: 0.3366 (mmp) REVERT: D 646 TYR cc_start: 0.7898 (t80) cc_final: 0.7673 (t80) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2797 time to fit residues: 122.8901 Evaluate side-chains 198 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 278 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 251 optimal weight: 0.0370 chunk 263 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22434 Z= 0.166 Angle : 0.576 10.787 30800 Z= 0.287 Chirality : 0.043 0.225 3810 Planarity : 0.004 0.062 3882 Dihedral : 6.443 73.702 3432 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -1.09 (0.16), residues: 3072 helix: 0.89 (0.16), residues: 1120 sheet: -1.91 (0.24), residues: 412 loop : -1.62 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 796 HIS 0.003 0.001 HIS C 162 PHE 0.035 0.001 PHE D 525 TYR 0.010 0.001 TYR B 167 ARG 0.009 0.001 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LEU cc_start: 0.7656 (pp) cc_final: 0.7442 (pp) REVERT: B 612 LEU cc_start: 0.7695 (tp) cc_final: 0.7264 (tp) REVERT: B 646 TYR cc_start: 0.7954 (t80) cc_final: 0.7719 (t80) REVERT: C 723 MET cc_start: 0.5189 (mmm) cc_final: 0.4716 (mmt) REVERT: D 112 LEU cc_start: 0.7782 (pp) cc_final: 0.7420 (pp) REVERT: D 142 MET cc_start: 0.4180 (mmm) cc_final: 0.3345 (mmp) REVERT: D 612 LEU cc_start: 0.7512 (tp) cc_final: 0.7197 (tp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2655 time to fit residues: 110.8225 Evaluate side-chains 194 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 308 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 245 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 150 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22434 Z= 0.152 Angle : 0.576 10.782 30800 Z= 0.285 Chirality : 0.043 0.215 3810 Planarity : 0.004 0.060 3882 Dihedral : 6.359 71.515 3432 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % 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: -1.00 (0.16), residues: 3072 helix: 0.95 (0.16), residues: 1116 sheet: -1.84 (0.26), residues: 388 loop : -1.58 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 796 HIS 0.002 0.000 HIS A 425 PHE 0.024 0.001 PHE B 563 TYR 0.010 0.001 TYR D 287 ARG 0.009 0.001 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 LEU cc_start: 0.7524 (pp) cc_final: 0.7296 (pp) REVERT: B 612 LEU cc_start: 0.7580 (tp) cc_final: 0.7325 (tp) REVERT: C 723 MET cc_start: 0.5066 (mmm) cc_final: 0.4654 (mmt) REVERT: D 112 LEU cc_start: 0.7755 (pp) cc_final: 0.7386 (pp) REVERT: D 142 MET cc_start: 0.4164 (mmm) cc_final: 0.3414 (mmp) REVERT: D 612 LEU cc_start: 0.7434 (tp) cc_final: 0.7174 (tp) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2646 time to fit residues: 110.6986 Evaluate side-chains 201 residues out of total 2702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 246 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 252 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.073948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059253 restraints weight = 126219.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060846 restraints weight = 76058.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.061917 restraints weight = 54116.424| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22434 Z= 0.136 Angle : 0.564 10.669 30800 Z= 0.277 Chirality : 0.042 0.205 3810 Planarity : 0.004 0.060 3882 Dihedral : 6.218 68.461 3432 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -0.95 (0.16), residues: 3072 helix: 0.93 (0.16), residues: 1138 sheet: -1.67 (0.25), residues: 430 loop : -1.55 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 796 HIS 0.002 0.000 HIS A 425 PHE 0.017 0.001 PHE D 525 TYR 0.010 0.001 TYR D 287 ARG 0.009 0.001 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.56 seconds wall clock time: 68 minutes 39.76 seconds (4119.76 seconds total)