Starting phenix.real_space_refine on Thu Mar 14 21:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/03_2024/7wi6_32526_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/03_2024/7wi6_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_32526/03_2024/7wi6_32526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/03_2024/7wi6_32526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/03_2024/7wi6_32526_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi6_32526/03_2024/7wi6_32526_updated.pdb" } resolution = 3.71 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= 0.000 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-dev-5265/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.84, per 1000 atoms: 0.60 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 2.5 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: 2.30 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: 2.60 Time building geometry restraints manager: 4.23 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 - 18.34: 5244 18.34 - 36.67: 488 36.67 - 55.01: 98 55.01 - 73.34: 12 73.34 - 91.68: 18 Dihedral angle restraints: 5860 sinusoidal: 1654 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 5857 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 7.270 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.460 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.690 ------------------------------------------------------------------------------- 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 : 15.694 91.675 3086 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 % Allowed : 14.10 % Favored : 84.36 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 297 HIS 0.007 0.002 HIS B 498 PHE 0.025 0.002 PHE B 456 TYR 0.021 0.002 TYR A 434 ARG 0.005 0.001 ARG B 183 *********************** 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 : 1.129 Fit side-chains REVERT: A 266 LYS cc_start: 0.8849 (mptt) cc_final: 0.8628 (mptt) REVERT: B 266 LYS cc_start: 0.8826 (mptt) cc_final: 0.8600 (mptt) REVERT: B 754 TYR cc_start: 0.6736 (t80) cc_final: 0.5443 (t80) outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 0.1914 time to fit residues: 31.1636 Evaluate side-chains 87 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 747 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 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: 0.9140 ------------------------------------------------------------------------------- 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 A 402 HIS B 108 GLN B 156 GLN B 386 GLN B 402 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1232 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= 0.229 Angle : 0.618 7.739 13580 Z= 0.334 Chirality : 0.043 0.177 1688 Planarity : 0.004 0.042 1736 Dihedral : 10.872 94.249 1598 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.31 % Allowed : 22.05 % Favored : 75.64 % 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: -5.61 (0.18), residues: 1418 helix: -4.20 (0.13), residues: 518 sheet: -3.30 (0.38), residues: 154 loop : -3.50 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 529 HIS 0.003 0.001 HIS B 485 PHE 0.010 0.001 PHE A 456 TYR 0.023 0.001 TYR B 434 ARG 0.001 0.000 ARG A 282 *********************** 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 107 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.081 Fit side-chains REVERT: B 391 MET cc_start: 0.8445 (tmm) cc_final: 0.8209 (tmm) REVERT: B 754 TYR cc_start: 0.6496 (t80) cc_final: 0.5156 (t80) outliers start: 18 outliers final: 9 residues processed: 105 average time/residue: 0.1638 time to fit residues: 26.4214 Evaluate side-chains 80 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 813 VAL 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: 0.0040 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 0.0020 chunk 131 optimal weight: 0.0870 chunk 141 optimal weight: 0.0030 chunk 116 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9886 Z= 0.138 Angle : 0.549 6.501 13580 Z= 0.295 Chirality : 0.041 0.138 1688 Planarity : 0.004 0.039 1736 Dihedral : 9.564 94.252 1598 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.59 % Allowed : 22.05 % Favored : 74.36 % 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: -5.14 (0.19), residues: 1418 helix: -3.72 (0.16), residues: 530 sheet: -2.86 (0.43), residues: 116 loop : -3.34 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 529 HIS 0.004 0.001 HIS A 498 PHE 0.008 0.001 PHE B 789 TYR 0.015 0.001 TYR A 434 ARG 0.002 0.000 ARG A 101 *********************** 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 122 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 0.882 Fit side-chains REVERT: A 355 TRP cc_start: 0.9097 (t-100) cc_final: 0.8336 (t-100) REVERT: A 391 MET cc_start: 0.8527 (tmm) cc_final: 0.8299 (ttp) REVERT: B 355 TRP cc_start: 0.9089 (t-100) cc_final: 0.8327 (t-100) REVERT: B 754 TYR cc_start: 0.6373 (t80) cc_final: 0.5077 (t80) outliers start: 28 outliers final: 15 residues processed: 118 average time/residue: 0.1413 time to fit residues: 27.3125 Evaluate side-chains 97 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.0050 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9886 Z= 0.383 Angle : 0.657 7.241 13580 Z= 0.340 Chirality : 0.047 0.226 1688 Planarity : 0.004 0.040 1736 Dihedral : 10.543 95.755 1594 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 3.59 % Allowed : 27.05 % Favored : 69.36 % 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: -4.81 (0.20), residues: 1418 helix: -3.45 (0.17), residues: 538 sheet: -2.46 (0.52), residues: 84 loop : -3.17 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 529 HIS 0.004 0.001 HIS B 485 PHE 0.017 0.002 PHE B 456 TYR 0.023 0.002 TYR B 434 ARG 0.003 0.001 ARG B 183 *********************** 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 108 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 1.040 Fit side-chains REVERT: A 391 MET cc_start: 0.8589 (tmm) cc_final: 0.8343 (tmm) REVERT: B 754 TYR cc_start: 0.6341 (t80) cc_final: 0.4985 (t80) outliers start: 28 outliers final: 24 residues processed: 107 average time/residue: 0.1459 time to fit residues: 25.3535 Evaluate side-chains 99 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL 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: 0.9980 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 0.3980 chunk 96 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2128 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= 0.180 Angle : 0.552 7.032 13580 Z= 0.289 Chirality : 0.042 0.155 1688 Planarity : 0.004 0.037 1736 Dihedral : 9.696 93.608 1594 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.97 % Allowed : 27.05 % Favored : 68.97 % 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: -4.61 (0.20), residues: 1418 helix: -3.26 (0.18), residues: 534 sheet: -2.70 (0.45), residues: 116 loop : -3.01 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 529 HIS 0.003 0.001 HIS B 498 PHE 0.007 0.001 PHE A 456 TYR 0.017 0.001 TYR A 434 ARG 0.001 0.000 ARG B 282 *********************** 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 121 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 90 time to evaluate : 1.033 Fit side-chains REVERT: A 391 MET cc_start: 0.8724 (tmm) cc_final: 0.8386 (tmm) outliers start: 31 outliers final: 27 residues processed: 118 average time/residue: 0.1609 time to fit residues: 29.7886 Evaluate side-chains 110 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 83 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2230 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= 0.225 Angle : 0.556 7.095 13580 Z= 0.289 Chirality : 0.043 0.144 1688 Planarity : 0.004 0.039 1736 Dihedral : 9.774 93.989 1594 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 5.64 % Allowed : 26.41 % Favored : 67.95 % 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: -4.52 (0.21), residues: 1418 helix: -3.13 (0.19), residues: 532 sheet: -2.67 (0.44), residues: 134 loop : -2.99 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.002 0.001 HIS B 485 PHE 0.010 0.001 PHE B 456 TYR 0.017 0.001 TYR B 434 ARG 0.002 0.000 ARG B 183 *********************** 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 131 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 1.163 Fit side-chains outliers start: 44 outliers final: 36 residues processed: 125 average time/residue: 0.1545 time to fit residues: 30.4528 Evaluate side-chains 122 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 86 optimal weight: 0.0060 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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: 0.7483 moved from start: 0.2487 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= 0.151 Angle : 0.520 7.170 13580 Z= 0.272 Chirality : 0.041 0.147 1688 Planarity : 0.003 0.037 1736 Dihedral : 9.235 93.275 1594 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.62 % Allowed : 27.82 % Favored : 67.56 % 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: -2.97 (0.19), residues: 520 sheet: -2.78 (0.38), residues: 162 loop : -2.74 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 529 HIS 0.003 0.001 HIS A 498 PHE 0.008 0.001 PHE A 630 TYR 0.014 0.001 TYR A 434 ARG 0.001 0.000 ARG B 282 *********************** 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 130 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 1.176 Fit side-chains REVERT: A 391 MET cc_start: 0.8613 (tmm) cc_final: 0.8389 (ttp) REVERT: B 754 TYR cc_start: 0.7887 (t80) cc_final: 0.7665 (t80) outliers start: 36 outliers final: 27 residues processed: 128 average time/residue: 0.1628 time to fit residues: 32.5192 Evaluate side-chains 112 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 813 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.0170 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9886 Z= 0.224 Angle : 0.551 6.986 13580 Z= 0.287 Chirality : 0.043 0.137 1688 Planarity : 0.004 0.038 1736 Dihedral : 9.481 94.053 1594 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 4.62 % Allowed : 28.08 % Favored : 67.31 % 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: -4.20 (0.21), residues: 1418 helix: -2.92 (0.20), residues: 520 sheet: -2.78 (0.39), residues: 162 loop : -2.67 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 529 HIS 0.002 0.001 HIS B 498 PHE 0.009 0.001 PHE B 456 TYR 0.014 0.001 TYR A 434 ARG 0.002 0.000 ARG A 189 *********************** 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 123 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 1.026 Fit side-chains REVERT: B 628 MET cc_start: 0.6514 (tpt) cc_final: 0.6263 (tpt) outliers start: 36 outliers final: 33 residues processed: 121 average time/residue: 0.1657 time to fit residues: 31.9930 Evaluate side-chains 120 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 87 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 747 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 116 optimal weight: 40.0000 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9886 Z= 0.281 Angle : 0.584 7.338 13580 Z= 0.303 Chirality : 0.044 0.153 1688 Planarity : 0.004 0.038 1736 Dihedral : 9.850 93.128 1594 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 4.36 % Allowed : 27.82 % Favored : 67.82 % 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: -4.19 (0.21), residues: 1418 helix: -2.93 (0.19), residues: 522 sheet: -2.88 (0.39), residues: 162 loop : -2.62 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 529 HIS 0.003 0.001 HIS B 498 PHE 0.011 0.001 PHE A 456 TYR 0.018 0.001 TYR B 434 ARG 0.002 0.000 ARG A 189 *********************** 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 122 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.084 Fit side-chains outliers start: 34 outliers final: 33 residues processed: 120 average time/residue: 0.1474 time to fit residues: 28.5317 Evaluate side-chains 121 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 303 TRP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 498 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 303 TRP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 747 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9886 Z= 0.419 Angle : 0.664 7.491 13580 Z= 0.343 Chirality : 0.047 0.213 1688 Planarity : 0.004 0.039 1736 Dihedral : 10.475 92.134 1594 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 4.36 % Allowed : 27.69 % Favored : 67.95 % 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: -4.12 (0.21), residues: 1418 helix: -2.96 (0.19), residues: 520 sheet: -2.48 (0.51), residues: 100 loop : -2.66 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 486 HIS 0.005 0.001 HIS B 498 PHE 0.016 0.002 PHE B 456 TYR 0.020 0.002 TYR B 434 ARG 0.003 0.001 ARG A 162 ********************** 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 121 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 1.115 Fit side-chains outliers start: 34 outliers final: 31 residues processed: 119 average time/residue: 0.1495 time to fit residues: 28.6634 Evaluate side-chains 118 residues out of total 1258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 87 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 747 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 105 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.157629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098747 restraints weight = 17388.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101197 restraints weight = 9591.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.102861 restraints weight = 6777.839| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2720 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= 0.175 Angle : 0.549 8.106 13580 Z= 0.287 Chirality : 0.042 0.153 1688 Planarity : 0.003 0.035 1736 Dihedral : 9.605 89.377 1594 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.85 % Allowed : 28.46 % Favored : 67.69 % 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: -4.10 (0.22), residues: 1418 helix: -2.81 (0.20), residues: 534 sheet: -2.90 (0.39), residues: 162 loop : -2.56 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 529 HIS 0.003 0.001 HIS A 498 PHE 0.009 0.001 PHE A 456 TYR 0.019 0.001 TYR B 434 ARG 0.001 0.000 ARG B 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.49 seconds wall clock time: 34 minutes 23.61 seconds (2063.61 seconds total)