Starting phenix.real_space_refine on Thu Jan 18 20:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi8_32527/01_2024/7wi8_32527_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi8_32527/01_2024/7wi8_32527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi8_32527/01_2024/7wi8_32527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi8_32527/01_2024/7wi8_32527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi8_32527/01_2024/7wi8_32527_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wi8_32527/01_2024/7wi8_32527_updated.pdb" } resolution = 4.17 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= 0.014 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 50 5.16 5 C 5884 2.51 5 N 1600 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9268 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4594 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 295} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain breaks: 5 Unresolved non-hydrogen bonds: 1171 Unresolved non-hydrogen angles: 1485 Unresolved non-hydrogen dihedrals: 987 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 16, 'ASN:plan1': 16, 'TRP:plan': 6, 'ASP:plan': 27, 'PHE:plan': 17, 'GLU:plan': 31, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 711 Chain: "B" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 4594 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 295} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain breaks: 5 Unresolved non-hydrogen bonds: 1171 Unresolved non-hydrogen angles: 1485 Unresolved non-hydrogen dihedrals: 987 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 16, 'ASN:plan1': 16, 'TRP:plan': 6, 'ASP:plan': 27, 'PHE:plan': 17, 'GLU:plan': 31, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 711 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: 5.30, per 1000 atoms: 0.57 Number of scatterers: 9268 At special positions: 0 Unit cell: (118.17, 87.87, 178.77, 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 50 16.00 O 1734 8.00 N 1600 7.00 C 5884 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=2.04 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 419 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A 730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 527 " distance=2.04 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 730 " 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 901 " - " ASN A 209 " " NAG B 901 " - " ASN B 209 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 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: 62 helices and 6 sheets defined 34.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 66 through 79 removed outlier: 4.057A pdb=" N ILE A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.965A pdb=" N GLU A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 112 " --> pdb=" O GLN A 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 205 through 208 No H-bonds generated for 'chain 'A' and resid 205 through 208' Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.695A pdb=" N GLU A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 285 through 291 removed outlier: 4.607A pdb=" N ARG A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.619A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.024A pdb=" N GLU A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 359 " --> pdb=" O TRP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.517A pdb=" N VAL A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.366A pdb=" N ALA A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.545A pdb=" N LYS A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 434' 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 579 through 588 removed outlier: 4.122A pdb=" N CYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 586 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 587 " --> pdb=" O ILE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.777A pdb=" N VAL A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 590 through 594' Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.789A pdb=" N MET A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR A 629 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 652 through 655 No H-bonds generated for 'chain 'A' and resid 652 through 655' Processing helix chain 'A' and resid 657 through 666 removed outlier: 3.565A pdb=" N THR A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 666 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 694 removed outlier: 3.845A pdb=" N CYS A 692 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 694 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 4.342A pdb=" N VAL A 701 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET A 702 " --> pdb=" O GLN A 699 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 703 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.530A pdb=" N LEU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 Processing helix chain 'A' and resid 750 through 759 removed outlier: 4.359A pdb=" N TYR A 754 " --> pdb=" O CYS A 751 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 755 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 756 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 757 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 758 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 759 " --> pdb=" O PHE A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 790 removed outlier: 3.950A pdb=" N TYR A 776 " --> pdb=" O GLY A 772 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 786 " --> pdb=" O TRP A 782 " (cutoff:3.500A) Proline residue: A 787 - end of helix removed outlier: 4.011A pdb=" N TYR A 790 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 removed outlier: 4.405A pdb=" N THR A 802 " --> pdb=" O VAL A 798 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 removed outlier: 4.076A pdb=" N PHE A 819 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 79 removed outlier: 4.056A pdb=" N ILE B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 78 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 removed outlier: 3.965A pdb=" N GLU B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 223 through 232 removed outlier: 3.696A pdb=" N GLU B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 285 through 291 removed outlier: 4.605A pdb=" N ARG B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.619A pdb=" N ARG B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 removed outlier: 4.024A pdb=" N GLU B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE B 359 " --> pdb=" O TRP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 removed outlier: 3.517A pdb=" N VAL B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.365A pdb=" N ALA B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 410 No H-bonds generated for 'chain 'B' and resid 407 through 410' Processing helix chain 'B' and resid 428 through 434 removed outlier: 3.545A pdb=" N LYS B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 434' 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 579 through 588 removed outlier: 4.122A pdb=" N CYS B 585 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 587 " --> pdb=" O ILE B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.778A pdb=" N VAL B 594 " --> pdb=" O CYS B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 590 through 594' Processing helix chain 'B' and resid 614 through 618 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.788A pdb=" N MET B 628 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR B 629 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 652 through 655 No H-bonds generated for 'chain 'B' and resid 652 through 655' Processing helix chain 'B' and resid 657 through 666 removed outlier: 3.565A pdb=" N THR B 661 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS B 662 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS B 665 " --> pdb=" O THR B 661 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 666 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 694 removed outlier: 3.846A pdb=" N CYS B 692 " --> pdb=" O VAL B 689 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY B 694 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.342A pdb=" N VAL B 701 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET B 702 " --> pdb=" O GLN B 699 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 703 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.530A pdb=" N LEU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 747 Processing helix chain 'B' and resid 750 through 759 removed outlier: 4.358A pdb=" N TYR B 754 " --> pdb=" O CYS B 751 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 755 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 756 " --> pdb=" O VAL B 753 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 757 " --> pdb=" O TYR B 754 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 758 " --> pdb=" O ALA B 755 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 759 " --> pdb=" O PHE B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 790 removed outlier: 3.950A pdb=" N TYR B 776 " --> pdb=" O GLY B 772 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 781 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B 786 " --> pdb=" O TRP B 782 " (cutoff:3.500A) Proline residue: B 787 - end of helix removed outlier: 4.010A pdb=" N TYR B 790 " --> pdb=" O LEU B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 813 removed outlier: 4.405A pdb=" N THR B 802 " --> pdb=" O VAL B 798 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY B 811 " --> pdb=" O VAL B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 820 removed outlier: 4.076A pdb=" N PHE B 819 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 3.529A pdb=" N ILE A 33 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 39 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N HIS A 94 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 41 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 244 through 246 removed outlier: 7.613A pdb=" N THR A 215 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR A 296 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU A 274 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 298 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 323 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 removed outlier: 4.046A pdb=" N HIS A 485 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.530A pdb=" N ILE B 33 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 244 through 246 removed outlier: 7.613A pdb=" N THR B 215 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR B 296 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU B 274 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 298 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 323 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 484 through 486 removed outlier: 4.046A pdb=" N HIS B 485 " --> pdb=" O SER B 491 " (cutoff:3.500A) 178 hydrogen bonds defined for protein. 432 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: 2.75 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3081 1.34 - 1.46: 2061 1.46 - 1.58: 4232 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 9436 Sorted by residual: bond pdb=" CAT Z99 A 902 " pdb=" OAP Z99 A 902 " ideal model delta sigma weight residual 1.364 1.483 -0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" CAT Z99 B 902 " pdb=" OAP Z99 B 902 " ideal model delta sigma weight residual 1.364 1.482 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" CAS Z99 B 902 " pdb=" OAP Z99 B 902 " ideal model delta sigma weight residual 1.369 1.485 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" CAS Z99 A 902 " pdb=" OAP Z99 A 902 " ideal model delta sigma weight residual 1.369 1.484 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" CAN Z99 B 902 " pdb=" CAW Z99 B 902 " ideal model delta sigma weight residual 1.543 1.612 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 9431 not shown) Histogram of bond angle deviations from ideal: 59.86 - 74.71: 6 74.71 - 89.55: 0 89.55 - 104.40: 154 104.40 - 119.25: 7698 119.25 - 134.10: 5154 Bond angle restraints: 13012 Sorted by residual: angle pdb=" C LYS A 822 " pdb=" N VAL A 823 " pdb=" CA VAL A 823 " ideal model delta sigma weight residual 121.70 128.62 -6.92 1.80e+00 3.09e-01 1.48e+01 angle pdb=" C LEU A 728 " pdb=" N LYS A 729 " pdb=" CA LYS A 729 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C LEU B 728 " pdb=" N LYS B 729 " pdb=" CA LYS B 729 " ideal model delta sigma weight residual 121.54 128.84 -7.30 1.91e+00 2.74e-01 1.46e+01 angle pdb=" C LYS B 822 " pdb=" N VAL B 823 " pdb=" CA VAL B 823 " ideal model delta sigma weight residual 121.70 128.57 -6.87 1.80e+00 3.09e-01 1.46e+01 angle pdb=" N ILE A 771 " pdb=" CA ILE A 771 " pdb=" C ILE A 771 " ideal model delta sigma weight residual 112.96 109.27 3.69 1.00e+00 1.00e+00 1.36e+01 ... (remaining 13007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 5197 19.94 - 39.87: 327 39.87 - 59.81: 51 59.81 - 79.74: 16 79.74 - 99.68: 3 Dihedral angle restraints: 5594 sinusoidal: 1394 harmonic: 4200 Sorted by residual: dihedral pdb=" CA GLY B 476 " pdb=" C GLY B 476 " pdb=" N LYS B 477 " pdb=" CA LYS B 477 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLY A 476 " pdb=" C GLY A 476 " pdb=" N LYS A 477 " pdb=" CA LYS A 477 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE A 239 " pdb=" C ILE A 239 " pdb=" N CYS A 240 " pdb=" CA CYS A 240 " ideal model delta harmonic sigma weight residual 180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 5591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1390 0.076 - 0.152: 224 0.152 - 0.229: 14 0.229 - 0.305: 6 0.305 - 0.381: 4 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CAY Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAR Z99 A 902 " pdb=" CAZ Z99 A 902 " both_signs ideal model delta sigma weight residual False -2.97 -2.59 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CAY Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAR Z99 B 902 " pdb=" CAZ Z99 B 902 " both_signs ideal model delta sigma weight residual False -2.97 -2.59 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CAZ Z99 A 902 " pdb=" CAO Z99 A 902 " pdb=" CAX Z99 A 902 " pdb=" CAY Z99 A 902 " both_signs ideal model delta sigma weight residual True 2.39 -2.72 -0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 1635 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 554 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 555 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 555 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 555 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 554 " -0.042 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 555 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 555 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 555 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ILE A 146 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 147 " -0.014 2.00e-02 2.50e+03 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3401 2.83 - 3.35: 8301 3.35 - 3.87: 14391 3.87 - 4.38: 15309 4.38 - 4.90: 25072 Nonbonded interactions: 66474 Sorted by model distance: nonbonded pdb=" O SER A 281 " pdb=" OG SER A 281 " model vdw 2.315 2.440 nonbonded pdb=" O SER B 281 " pdb=" OG SER B 281 " model vdw 2.316 2.440 nonbonded pdb=" N ASP A 461 " pdb=" OD1 ASP A 461 " model vdw 2.325 2.520 nonbonded pdb=" N ASP B 461 " pdb=" OD1 ASP B 461 " model vdw 2.326 2.520 nonbonded pdb=" O THR A 174 " pdb=" OG1 THR A 174 " model vdw 2.332 2.440 ... (remaining 66469 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: 1.370 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: 0.010 Extract box with map and model: 7.180 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.150 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.008 0.119 9436 Z= 0.525 Angle : 1.003 9.504 13012 Z= 0.540 Chirality : 0.060 0.381 1638 Planarity : 0.006 0.063 1702 Dihedral : 14.718 99.676 2820 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.21 % Favored : 85.65 % Rotamer: Outliers : 1.22 % Allowed : 17.89 % Favored : 80.89 % 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: -5.88 (0.16), residues: 1422 helix: -4.77 (0.09), residues: 428 sheet: -3.93 (0.37), residues: 108 loop : -3.62 (0.17), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 210 HIS 0.003 0.001 HIS A 94 PHE 0.021 0.002 PHE A 456 TYR 0.025 0.003 TYR A 434 ARG 0.003 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.942 Fit side-chains REVERT: A 391 MET cc_start: 0.7130 (tmm) cc_final: 0.6911 (tmm) outliers start: 8 outliers final: 0 residues processed: 61 average time/residue: 0.1552 time to fit residues: 15.3649 Evaluate side-chains 49 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 0.9980 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 30.0000 chunk 112 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 130 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9436 Z= 0.153 Angle : 0.580 5.867 13012 Z= 0.305 Chirality : 0.043 0.167 1638 Planarity : 0.004 0.044 1702 Dihedral : 9.008 100.411 1580 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % 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: -4.97 (0.18), residues: 1422 helix: -3.48 (0.16), residues: 508 sheet: -3.70 (0.37), residues: 120 loop : -3.17 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 529 HIS 0.001 0.000 HIS A 498 PHE 0.014 0.001 PHE A 112 TYR 0.012 0.001 TYR A 434 ARG 0.002 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1546 time to fit residues: 16.6380 Evaluate side-chains 48 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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: 10.0000 chunk 40 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.0040 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 0.0050 chunk 105 optimal weight: 0.0870 overall best weight: 0.2384 ------------------------------------------------------------------------------- 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: 0.7526 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9436 Z= 0.122 Angle : 0.536 5.019 13012 Z= 0.277 Chirality : 0.042 0.136 1638 Planarity : 0.004 0.039 1702 Dihedral : 8.402 102.061 1580 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: -4.16 (0.20), residues: 1422 helix: -2.56 (0.20), residues: 498 sheet: -3.08 (0.46), residues: 90 loop : -2.96 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 303 HIS 0.001 0.000 HIS A 94 PHE 0.005 0.001 PHE A 456 TYR 0.013 0.001 TYR B 222 ARG 0.001 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1530 time to fit residues: 16.8126 Evaluate side-chains 53 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 40.0000 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 4.8126 ------------------------------------------------------------------------------- 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: 0.7792 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9436 Z= 0.498 Angle : 0.772 6.665 13012 Z= 0.404 Chirality : 0.049 0.193 1638 Planarity : 0.005 0.060 1702 Dihedral : 8.868 101.527 1580 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.68 % Favored : 84.32 % Rotamer: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % 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: -4.25 (0.20), residues: 1422 helix: -2.59 (0.21), residues: 486 sheet: -3.40 (0.45), residues: 88 loop : -3.03 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 303 HIS 0.010 0.002 HIS A 498 PHE 0.025 0.003 PHE A 456 TYR 0.029 0.003 TYR B 434 ARG 0.007 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1883 time to fit residues: 16.0036 Evaluate side-chains 50 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 96 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9436 Z= 0.188 Angle : 0.574 6.311 13012 Z= 0.297 Chirality : 0.043 0.136 1638 Planarity : 0.004 0.037 1702 Dihedral : 7.725 99.766 1580 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % 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: -3.75 (0.21), residues: 1422 helix: -2.07 (0.22), residues: 476 sheet: -3.21 (0.42), residues: 108 loop : -2.74 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 529 HIS 0.002 0.001 HIS B 498 PHE 0.010 0.001 PHE B 440 TYR 0.017 0.001 TYR B 434 ARG 0.003 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1912 time to fit residues: 17.6913 Evaluate side-chains 48 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 20.0000 chunk 125 optimal weight: 0.6980 chunk 27 optimal weight: 0.0030 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9436 Z= 0.276 Angle : 0.618 6.231 13012 Z= 0.324 Chirality : 0.045 0.146 1638 Planarity : 0.005 0.040 1702 Dihedral : 8.091 97.887 1580 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -3.68 (0.21), residues: 1422 helix: -2.02 (0.22), residues: 494 sheet: -3.12 (0.47), residues: 88 loop : -2.74 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 529 HIS 0.004 0.001 HIS B 498 PHE 0.015 0.002 PHE B 456 TYR 0.020 0.002 TYR B 434 ARG 0.005 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1557 time to fit residues: 13.9552 Evaluate side-chains 47 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9436 Z= 0.251 Angle : 0.616 6.354 13012 Z= 0.320 Chirality : 0.045 0.184 1638 Planarity : 0.004 0.038 1702 Dihedral : 7.961 96.636 1580 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -3.47 (0.22), residues: 1422 helix: -1.78 (0.23), residues: 482 sheet: -3.09 (0.47), residues: 88 loop : -2.64 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 529 HIS 0.004 0.001 HIS A 498 PHE 0.013 0.002 PHE A 456 TYR 0.019 0.002 TYR A 434 ARG 0.005 0.001 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.084 Fit side-chains REVERT: A 391 MET cc_start: 0.7537 (tmm) cc_final: 0.7312 (tmm) REVERT: B 391 MET cc_start: 0.7518 (tmm) cc_final: 0.7298 (tmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1199 time to fit residues: 11.3950 Evaluate side-chains 45 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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: 7.9990 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 0.0470 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9436 Z= 0.151 Angle : 0.568 6.014 13012 Z= 0.291 Chirality : 0.043 0.165 1638 Planarity : 0.004 0.039 1702 Dihedral : 7.415 97.108 1580 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -3.34 (0.22), residues: 1422 helix: -1.67 (0.23), residues: 496 sheet: -3.04 (0.46), residues: 92 loop : -2.55 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 529 HIS 0.002 0.001 HIS A 498 PHE 0.022 0.001 PHE A 471 TYR 0.015 0.001 TYR B 434 ARG 0.002 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.061 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1254 time to fit residues: 13.1817 Evaluate side-chains 50 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 0.0000 chunk 129 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 101 optimal weight: 0.0370 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.1266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.002 0.023 9436 Z= 0.157 Angle : 0.560 5.696 13012 Z= 0.287 Chirality : 0.043 0.238 1638 Planarity : 0.004 0.042 1702 Dihedral : 7.310 96.995 1580 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -3.17 (0.22), residues: 1422 helix: -1.47 (0.23), residues: 504 sheet: -2.92 (0.47), residues: 92 loop : -2.50 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 529 HIS 0.002 0.001 HIS B 498 PHE 0.010 0.001 PHE B 456 TYR 0.017 0.001 TYR B 434 ARG 0.002 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.075 Fit side-chains REVERT: A 391 MET cc_start: 0.7261 (tmm) cc_final: 0.7030 (tmm) REVERT: B 391 MET cc_start: 0.7233 (tmm) cc_final: 0.6996 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1184 time to fit residues: 12.0384 Evaluate side-chains 49 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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: 10.0000 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 9436 Z= 0.487 Angle : 0.777 6.703 13012 Z= 0.408 Chirality : 0.051 0.238 1638 Planarity : 0.005 0.046 1702 Dihedral : 8.823 94.959 1580 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 16.67 % Favored : 83.26 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: -3.49 (0.22), residues: 1422 helix: -1.84 (0.23), residues: 496 sheet: -3.04 (0.48), residues: 88 loop : -2.63 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 486 HIS 0.008 0.002 HIS A 498 PHE 0.032 0.003 PHE B 471 TYR 0.037 0.003 TYR A 434 ARG 0.010 0.001 ARG B 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.061 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1192 time to fit residues: 11.3817 Evaluate side-chains 45 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.093273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067897 restraints weight = 33023.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066427 restraints weight = 24479.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066814 restraints weight = 22155.615| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9436 Z= 0.220 Angle : 0.616 6.949 13012 Z= 0.319 Chirality : 0.045 0.237 1638 Planarity : 0.004 0.036 1702 Dihedral : 7.873 94.533 1580 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.24 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -3.27 (0.22), residues: 1422 helix: -1.65 (0.23), residues: 510 sheet: -2.89 (0.49), residues: 88 loop : -2.52 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 486 HIS 0.003 0.001 HIS B 498 PHE 0.027 0.001 PHE B 471 TYR 0.021 0.002 TYR B 434 ARG 0.004 0.001 ARG B 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1605.46 seconds wall clock time: 29 minutes 48.79 seconds (1788.79 seconds total)