Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:13:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/04_2023/7wi6_32526_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/04_2023/7wi6_32526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/04_2023/7wi6_32526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/04_2023/7wi6_32526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/04_2023/7wi6_32526_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/04_2023/7wi6_32526_updated.pdb" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 104 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6206 2.51 5 N 1638 2.21 5 O 1786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9696 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4808 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain breaks: 6 Unresolved non-hydrogen bonds: 945 Unresolved non-hydrogen angles: 1197 Unresolved non-hydrogen dihedrals: 794 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 5, 'ASP:plan': 28, 'PHE:plan': 11, 'GLU:plan': 30, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 608 Chain: "B" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4808 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 232} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain breaks: 6 Unresolved non-hydrogen bonds: 945 Unresolved non-hydrogen angles: 1197 Unresolved non-hydrogen dihedrals: 794 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 5, 'ASP:plan': 28, 'PHE:plan': 11, 'GLU:plan': 30, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 608 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.97, per 1000 atoms: 0.62 Number of scatterers: 9696 At special positions: 0 Unit cell: (95.95, 97.97, 181.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1786 8.00 N 1638 7.00 C 6206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 527 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 373 " distance=2.02 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 513 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.02 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 546 " distance=2.04 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 209 " " NAG B 902 " - " ASN B 209 " Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 10 sheets defined 27.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 66 through 81 removed outlier: 4.073A pdb=" N ALA A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 4.508A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 258 through 261 No H-bonds generated for 'chain 'A' and resid 258 through 261' Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.745A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 394 through 398 removed outlier: 3.766A pdb=" N TYR A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 398' Processing helix chain 'A' and resid 400 through 408 removed outlier: 4.383A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.950A pdb=" N ASP A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.864A pdb=" N VAL A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.623A pdb=" N VAL A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.898A pdb=" N PHE A 620 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 621 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A 623 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 624 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER A 625 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.681A pdb=" N ARG A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 653 No H-bonds generated for 'chain 'A' and resid 650 through 653' Processing helix chain 'A' and resid 658 through 660 No H-bonds generated for 'chain 'A' and resid 658 through 660' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.785A pdb=" N LEU A 697 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN A 699 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 744 through 750 removed outlier: 3.728A pdb=" N LEU A 747 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 748 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'A' and resid 787 through 791 Processing helix chain 'A' and resid 798 through 801 No H-bonds generated for 'chain 'A' and resid 798 through 801' Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 817 through 819 No H-bonds generated for 'chain 'A' and resid 817 through 819' Processing helix chain 'B' and resid 66 through 81 removed outlier: 4.074A pdb=" N ALA B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 removed outlier: 4.508A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 258 through 261 No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 285 through 288 No H-bonds generated for 'chain 'B' and resid 285 through 288' Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.747A pdb=" N ARG B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 394 through 398 removed outlier: 3.766A pdb=" N TYR B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 394 through 398' Processing helix chain 'B' and resid 400 through 408 removed outlier: 4.383A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.951A pdb=" N ASP B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 577 through 587 removed outlier: 3.864A pdb=" N VAL B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.622A pdb=" N VAL B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 607 No H-bonds generated for 'chain 'B' and resid 605 through 607' Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.897A pdb=" N PHE B 620 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 621 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B 623 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU B 624 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N SER B 625 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 631 No H-bonds generated for 'chain 'B' and resid 629 through 631' Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.681A pdb=" N ARG B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 653 No H-bonds generated for 'chain 'B' and resid 650 through 653' Processing helix chain 'B' and resid 658 through 660 No H-bonds generated for 'chain 'B' and resid 658 through 660' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 692 through 700 removed outlier: 3.784A pdb=" N LEU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 699 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 744 through 750 removed outlier: 3.729A pdb=" N LEU B 747 " --> pdb=" O ASP B 744 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 748 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 775 No H-bonds generated for 'chain 'B' and resid 773 through 775' Processing helix chain 'B' and resid 779 through 783 Processing helix chain 'B' and resid 787 through 791 Processing helix chain 'B' and resid 798 through 801 No H-bonds generated for 'chain 'B' and resid 798 through 801' Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'B' and resid 817 through 819 No H-bonds generated for 'chain 'B' and resid 817 through 819' Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.710A pdb=" N ILE A 33 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N HIS A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 41 " --> pdb=" O HIS A 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 96 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY A 43 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.649A pdb=" N GLU A 245 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 247 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.785A pdb=" N THR A 296 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU A 274 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 298 " --> pdb=" O LEU A 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 322 through 325 Processing sheet with id= E, first strand: chain 'A' and resid 718 through 720 Processing sheet with id= F, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.710A pdb=" N ILE B 33 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.650A pdb=" N GLU B 245 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL B 247 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 271 through 274 removed outlier: 6.784A pdb=" N THR B 296 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 274 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 298 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 322 through 325 Processing sheet with id= J, first strand: chain 'B' and resid 718 through 720 122 hydrogen bonds defined for protein. 300 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: 2.53 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2487 1.33 - 1.45: 2165 1.45 - 1.58: 5148 1.58 - 1.70: 2 1.70 - 1.82: 84 Bond restraints: 9886 Sorted by residual: bond pdb=" CAT Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.364 1.492 -0.128 2.00e-02 2.50e+03 4.11e+01 bond pdb=" CAT Z99 A 901 " pdb=" OAP Z99 A 901 " ideal model delta sigma weight residual 1.364 1.492 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" CAS Z99 A 901 " pdb=" OAP Z99 A 901 " ideal model delta sigma weight residual 1.369 1.494 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" CAS Z99 B 901 " pdb=" OAP Z99 B 901 " ideal model delta sigma weight residual 1.369 1.493 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C LEU B 340 " pdb=" N ASN B 341 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.04e+01 ... (remaining 9881 not shown) Histogram of bond angle deviations from ideal: 59.86 - 74.71: 6 74.71 - 89.56: 0 89.56 - 104.40: 164 104.40 - 119.25: 8059 119.25 - 134.10: 5351 Bond angle restraints: 13580 Sorted by residual: angle pdb=" N ILE A 155 " pdb=" CA ILE A 155 " pdb=" C ILE A 155 " ideal model delta sigma weight residual 113.20 105.06 8.14 9.60e-01 1.09e+00 7.20e+01 angle pdb=" N ILE B 155 " pdb=" CA ILE B 155 " pdb=" C ILE B 155 " ideal model delta sigma weight residual 113.20 105.10 8.10 9.60e-01 1.09e+00 7.12e+01 angle pdb=" C GLY A 713 " pdb=" N THR A 714 " pdb=" CA THR A 714 " ideal model delta sigma weight residual 122.46 128.34 -5.88 1.41e+00 5.03e-01 1.74e+01 angle pdb=" C GLY B 713 " pdb=" N THR B 714 " pdb=" CA THR B 714 " ideal model delta sigma weight residual 122.46 128.25 -5.79 1.41e+00 5.03e-01 1.69e+01 angle pdb=" N VAL B 701 " pdb=" CA VAL B 701 " pdb=" C VAL B 701 " ideal model delta sigma weight residual 113.20 109.32 3.88 9.60e-01 1.09e+00 1.63e+01 ... (remaining 13575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 5130 16.63 - 33.26: 514 33.26 - 49.89: 106 49.89 - 66.52: 16 66.52 - 83.15: 10 Dihedral angle restraints: 5776 sinusoidal: 1570 harmonic: 4206 Sorted by residual: dihedral pdb=" CB CYS B 513 " pdb=" SG CYS B 513 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS A 513 " pdb=" SG CYS A 513 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual -86.00 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" CB CYS B 534 " pdb=" SG CYS B 534 " pdb=" SG CYS B 546 " pdb=" CB CYS B 546 " ideal model delta sinusoidal sigma weight residual 93.00 170.72 -77.72 1 1.00e+01 1.00e-02 7.56e+01 ... (remaining 5773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1410 0.077 - 0.153: 250 0.153 - 0.230: 14 0.230 - 0.307: 8 0.307 - 0.383: 6 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CAW Z99 B 901 " pdb=" CAN Z99 B 901 " pdb=" CAU Z99 B 901 " pdb=" CAV Z99 B 901 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CAW Z99 A 901 " pdb=" CAN Z99 A 901 " pdb=" CAU Z99 A 901 " pdb=" CAV Z99 A 901 " both_signs ideal model delta sigma weight residual False 2.61 2.23 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CAY Z99 B 901 " pdb=" CAN Z99 B 901 " pdb=" CAR Z99 B 901 " pdb=" CAZ Z99 B 901 " both_signs ideal model delta sigma weight residual False -2.97 -2.62 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 1685 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 146 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ILE B 146 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE B 146 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY B 147 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C ILE A 146 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY A 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ILE A 390 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 390 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 391 " -0.014 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3336 2.81 - 3.33: 8254 3.33 - 3.86: 14929 3.86 - 4.38: 15590 4.38 - 4.90: 26133 Nonbonded interactions: 68242 Sorted by model distance: nonbonded pdb=" OE1 GLN B 165 " pdb=" OH TYR B 186 " model vdw 2.290 2.440 nonbonded pdb=" OE1 GLN A 165 " pdb=" OH TYR A 186 " model vdw 2.290 2.440 nonbonded pdb=" O SER B 179 " pdb=" OG SER B 179 " model vdw 2.295 2.440 nonbonded pdb=" O SER A 179 " pdb=" OG SER A 179 " model vdw 2.295 2.440 nonbonded pdb=" O THR A 296 " pdb=" OG1 THR A 296 " model vdw 2.298 2.440 ... (remaining 68237 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 'B' } 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 7.660 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.560 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.128 9886 Z= 0.617 Angle : 1.017 8.446 13580 Z= 0.554 Chirality : 0.063 0.383 1688 Planarity : 0.006 0.056 1736 Dihedral : 14.548 78.703 3002 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -6.21 (0.16), residues: 1418 helix: -4.83 (0.09), residues: 512 sheet: -3.65 (0.35), residues: 154 loop : -3.75 (0.19), residues: 752 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.194 Fit side-chains outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 0.1986 time to fit residues: 32.4037 Evaluate side-chains 87 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0865 time to fit residues: 2.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 20.0000 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 0.0770 chunk 130 optimal weight: 3.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 156 GLN A 386 GLN B 108 GLN B 156 GLN B 386 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9886 Z= 0.206 Angle : 0.610 7.521 13580 Z= 0.329 Chirality : 0.043 0.169 1688 Planarity : 0.004 0.042 1736 Dihedral : 7.651 65.891 1506 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -5.57 (0.18), residues: 1418 helix: -4.19 (0.13), residues: 518 sheet: -3.23 (0.38), residues: 154 loop : -3.47 (0.21), residues: 746 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.194 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.1743 time to fit residues: 27.6179 Evaluate side-chains 80 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0860 time to fit residues: 2.5152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 30.0000 chunk 141 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 9886 Z= 0.244 Angle : 0.600 6.699 13580 Z= 0.318 Chirality : 0.044 0.214 1688 Planarity : 0.004 0.037 1736 Dihedral : 7.290 64.028 1506 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.19), residues: 1418 helix: -3.63 (0.17), residues: 512 sheet: -2.94 (0.44), residues: 128 loop : -3.29 (0.21), residues: 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.184 Fit side-chains outliers start: 26 outliers final: 14 residues processed: 104 average time/residue: 0.1596 time to fit residues: 26.5393 Evaluate side-chains 93 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0943 time to fit residues: 3.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 139 optimal weight: 0.0870 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9886 Z= 0.234 Angle : 0.580 6.021 13580 Z= 0.304 Chirality : 0.043 0.193 1688 Planarity : 0.004 0.036 1736 Dihedral : 7.038 64.025 1506 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.20), residues: 1418 helix: -3.44 (0.18), residues: 526 sheet: -2.98 (0.43), residues: 116 loop : -3.18 (0.22), residues: 776 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.163 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.1596 time to fit residues: 26.0300 Evaluate side-chains 88 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1052 time to fit residues: 3.9399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 57 optimal weight: 0.0870 chunk 118 optimal weight: 0.4980 chunk 96 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN A 402 HIS B 402 HIS B 498 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9886 Z= 0.164 Angle : 0.537 5.535 13580 Z= 0.283 Chirality : 0.042 0.148 1688 Planarity : 0.003 0.037 1736 Dihedral : 6.646 63.491 1506 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.20), residues: 1418 helix: -3.19 (0.19), residues: 518 sheet: -2.70 (0.44), residues: 116 loop : -3.02 (0.22), residues: 784 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 1.158 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 0.1586 time to fit residues: 23.6436 Evaluate side-chains 85 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.159 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0929 time to fit residues: 2.2579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 0.0270 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 134 optimal weight: 20.0000 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9886 Z= 0.196 Angle : 0.551 7.405 13580 Z= 0.285 Chirality : 0.043 0.181 1688 Planarity : 0.003 0.037 1736 Dihedral : 6.489 63.063 1506 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.21), residues: 1418 helix: -3.04 (0.19), residues: 516 sheet: -2.51 (0.47), residues: 116 loop : -2.80 (0.23), residues: 786 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.113 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 0.1639 time to fit residues: 24.8025 Evaluate side-chains 87 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0921 time to fit residues: 2.4375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 9886 Z= 0.154 Angle : 0.528 7.779 13580 Z= 0.274 Chirality : 0.042 0.156 1688 Planarity : 0.003 0.036 1736 Dihedral : 6.181 62.727 1506 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.21), residues: 1418 helix: -2.91 (0.20), residues: 520 sheet: -2.57 (0.44), residues: 136 loop : -2.68 (0.23), residues: 762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.257 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 97 average time/residue: 0.1642 time to fit residues: 25.9435 Evaluate side-chains 86 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1052 time to fit residues: 2.1824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.0970 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9886 Z= 0.172 Angle : 0.530 7.306 13580 Z= 0.275 Chirality : 0.042 0.150 1688 Planarity : 0.003 0.036 1736 Dihedral : 6.109 62.291 1506 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.22), residues: 1418 helix: -2.86 (0.20), residues: 520 sheet: -2.56 (0.44), residues: 136 loop : -2.50 (0.24), residues: 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.129 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 90 average time/residue: 0.1814 time to fit residues: 26.0694 Evaluate side-chains 86 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0942 time to fit residues: 1.8912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.3980 chunk 121 optimal weight: 0.1980 chunk 129 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 40.0000 chunk 122 optimal weight: 0.3980 chunk 128 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9886 Z= 0.138 Angle : 0.514 7.535 13580 Z= 0.267 Chirality : 0.042 0.138 1688 Planarity : 0.003 0.035 1736 Dihedral : 5.890 62.095 1506 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.22), residues: 1418 helix: -2.68 (0.21), residues: 508 sheet: -2.50 (0.42), residues: 148 loop : -2.33 (0.24), residues: 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.155 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 91 average time/residue: 0.1616 time to fit residues: 23.8996 Evaluate side-chains 87 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0894 time to fit residues: 1.9038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 132 optimal weight: 0.0270 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 70 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9886 Z= 0.221 Angle : 0.545 6.948 13580 Z= 0.282 Chirality : 0.043 0.174 1688 Planarity : 0.003 0.037 1736 Dihedral : 6.089 62.396 1506 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.22), residues: 1418 helix: -2.66 (0.21), residues: 508 sheet: -2.45 (0.41), residues: 162 loop : -2.34 (0.24), residues: 748 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 1.117 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1648 time to fit residues: 23.7805 Evaluate side-chains 87 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 0.0970 chunk 16 optimal weight: 0.0270 chunk 31 optimal weight: 0.2980 chunk 114 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.165420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109115 restraints weight = 17243.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109101 restraints weight = 10512.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.109083 restraints weight = 8116.894| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 9886 Z= 0.134 Angle : 0.511 6.325 13580 Z= 0.266 Chirality : 0.042 0.142 1688 Planarity : 0.003 0.035 1736 Dihedral : 5.838 62.345 1506 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.22), residues: 1418 helix: -2.55 (0.21), residues: 508 sheet: -2.45 (0.40), residues: 162 loop : -2.26 (0.25), residues: 748 =============================================================================== Job complete usr+sys time: 1782.34 seconds wall clock time: 33 minutes 7.77 seconds (1987.77 seconds total)