Starting phenix.real_space_refine on Fri Mar 14 04:16:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi8_32527/03_2025/7wi8_32527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi8_32527/03_2025/7wi8_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/cci-nas-00/data/ceres_data/7wi8_32527/03_2025/7wi8_32527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi8_32527/03_2025/7wi8_32527.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi8_32527/03_2025/7wi8_32527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi8_32527/03_2025/7wi8_32527.cif" } 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. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9268 Number of models: 1 Model: "" Number of chains: 2 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: "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 Restraints were copied for chains: B Time building chain proxies: 9.09, per 1000 atoms: 0.98 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 - 3.00 Amino acid : True - 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: 2.56 Conformation dependent library (CDL) restraints added in 1.4 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... Secondary structure from input PDB file: 65 helices and 6 sheets defined 40.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.556A pdb=" N LEU A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) 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 101 through 114 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) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.734A pdb=" N SER A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 203 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 222 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 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 286 removed outlier: 4.157A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.402A pdb=" N ALA A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 4.098A pdb=" N ASP A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 360 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 389 through 397 removed outlier: 3.517A pdb=" N VAL A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.686A pdb=" N ALA A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 427 through 435 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) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.759A pdb=" N THR A 582 " --> pdb=" O ILE A 578 " (cutoff:3.500A) 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 589 through 595 removed outlier: 3.917A pdb=" N MET A 593 " --> pdb=" O MET A 589 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 620 through 633 removed outlier: 3.845A pdb=" N LEU A 624 " --> pdb=" O PHE A 620 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A 630 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 removed outlier: 3.692A pdb=" N LEU A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 removed outlier: 3.959A pdb=" N SER A 650 " --> pdb=" O GLY A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 656 through 667 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 688 through 697 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) removed outlier: 4.208A pdb=" N ILE A 696 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 697 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 708 removed outlier: 3.888A pdb=" N MET A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 706 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.640A pdb=" N MET A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.696A pdb=" N VAL A 745 " --> pdb=" O LEU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 751 No H-bonds generated for 'chain 'A' and resid 749 through 751' Processing helix chain 'A' and resid 752 through 758 removed outlier: 3.881A pdb=" N PHE A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 757 " --> pdb=" O VAL A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 789 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 Processing helix chain 'A' and resid 795 through 814 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 814 through 820 removed outlier: 4.174A pdb=" N LEU A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 819 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.555A pdb=" N LEU B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) 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 101 through 114 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) Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.734A pdb=" N SER B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 203 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 222 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 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.157A pdb=" N ILE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.402A pdb=" N ALA B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 4.099A pdb=" N ASP B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 360 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 389 through 397 removed outlier: 3.517A pdb=" N VAL B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 removed outlier: 3.686A pdb=" N ALA B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 406 " --> pdb=" O HIS B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 427 through 435 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) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 578 through 589 removed outlier: 3.759A pdb=" N THR B 582 " --> pdb=" O ILE B 578 " (cutoff:3.500A) 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 589 through 595 removed outlier: 3.917A pdb=" N MET B 593 " --> pdb=" O MET B 589 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 594 " --> pdb=" O CYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 620 through 633 removed outlier: 3.846A pdb=" N LEU B 624 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 removed outlier: 3.693A pdb=" N LEU B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 Processing helix chain 'B' and resid 656 through 667 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 688 through 697 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) removed outlier: 4.209A pdb=" N ILE B 696 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B 697 " --> pdb=" O GLY B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 708 removed outlier: 3.889A pdb=" N MET B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 707 " --> pdb=" O VAL B 703 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.640A pdb=" N MET B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 748 removed outlier: 3.695A pdb=" N VAL B 745 " --> pdb=" O LEU B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 751 No H-bonds generated for 'chain 'B' and resid 749 through 751' Processing helix chain 'B' and resid 752 through 758 removed outlier: 3.882A pdb=" N PHE B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS B 757 " --> pdb=" O VAL B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 789 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 Processing helix chain 'B' and resid 795 through 814 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 814 through 820 removed outlier: 4.174A pdb=" N LEU B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE B 819 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing sheet with id=AA1, 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: 7.774A pdb=" N VAL A 40 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE A 146 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY A 42 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE A 169 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 246 removed outlier: 5.607A pdb=" N VAL A 213 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR A 243 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 215 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 245 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 217 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP A 297 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU A 323 " --> pdb=" O TRP A 297 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA A 299 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 10.249A pdb=" N LEU A 325 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 466 " --> pdb=" O HIS A 485 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N HIS A 485 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 468 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS A 485 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, 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: 7.774A pdb=" N VAL B 40 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE B 146 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY B 42 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE B 169 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 240 through 246 removed outlier: 5.607A pdb=" N VAL B 213 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 243 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 215 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 245 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 217 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TRP B 297 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N LEU B 323 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA B 299 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N LEU B 325 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR B 466 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N HIS B 485 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 468 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS B 485 " --> pdb=" O SER B 491 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 539 253 hydrogen bonds defined for protein. 711 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: 2.97 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: 0.00 - 1.90: 12280 1.90 - 3.80: 588 3.80 - 5.70: 88 5.70 - 7.60: 39 7.60 - 9.50: 17 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: 3367 2.83 - 3.35: 8257 3.35 - 3.87: 14293 3.87 - 4.38: 15211 4.38 - 4.90: 25046 Nonbonded interactions: 66174 Sorted by model distance: nonbonded pdb=" O SER A 281 " pdb=" OG SER A 281 " model vdw 2.315 3.040 nonbonded pdb=" O SER B 281 " pdb=" OG SER B 281 " model vdw 2.316 3.040 nonbonded pdb=" N ASP A 461 " pdb=" OD1 ASP A 461 " model vdw 2.325 3.120 nonbonded pdb=" N ASP B 461 " pdb=" OD1 ASP B 461 " model vdw 2.326 3.120 nonbonded pdb=" O THR A 174 " pdb=" OG1 THR A 174 " model vdw 2.332 3.040 ... (remaining 66169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.470 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- 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= 0.521 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 to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 1.196 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: 0.1700 time to fit residues: 17.3854 Evaluate side-chains 49 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 0.2980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.0010 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 30.0000 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.094951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071102 restraints weight = 31137.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069371 restraints weight = 22246.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069718 restraints weight = 25213.501| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9436 Z= 0.149 Angle : 0.606 6.291 13012 Z= 0.319 Chirality : 0.043 0.161 1638 Planarity : 0.004 0.044 1702 Dihedral : 8.957 100.482 1580 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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: -4.99 (0.18), residues: 1422 helix: -3.51 (0.15), residues: 496 sheet: -3.58 (0.38), residues: 108 loop : -3.24 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 297 HIS 0.001 0.000 HIS A 94 PHE 0.014 0.001 PHE A 112 TYR 0.013 0.001 TYR A 434 ARG 0.003 0.000 ARG A 644 *********************** 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 71 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 169 ILE cc_start: 0.8544 (mp) cc_final: 0.8327 (mm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2106 time to fit residues: 24.1739 Evaluate side-chains 44 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 105 optimal weight: 0.0070 chunk 129 optimal weight: 10.0000 chunk 74 optimal weight: 0.0030 chunk 125 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 114 optimal weight: 0.4980 chunk 100 optimal weight: 0.2980 overall best weight: 1.7610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.093001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.068027 restraints weight = 32220.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066207 restraints weight = 23279.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.066978 restraints weight = 23747.167| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9436 Z= 0.217 Angle : 0.604 6.180 13012 Z= 0.317 Chirality : 0.044 0.151 1638 Planarity : 0.004 0.038 1702 Dihedral : 8.612 101.006 1580 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % 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: -4.40 (0.19), residues: 1422 helix: -2.65 (0.20), residues: 482 sheet: -3.42 (0.40), residues: 108 loop : -3.15 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 303 HIS 0.002 0.001 HIS A 498 PHE 0.013 0.001 PHE A 456 TYR 0.019 0.002 TYR A 434 ARG 0.004 0.001 ARG B 645 *********************** 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 64 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2976 time to fit residues: 29.6668 Evaluate side-chains 44 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 108 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 61 optimal weight: 50.0000 chunk 129 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.090674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.066115 restraints weight = 32360.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063825 restraints weight = 23564.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064558 restraints weight = 23476.932| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9436 Z= 0.323 Angle : 0.671 6.683 13012 Z= 0.350 Chirality : 0.046 0.162 1638 Planarity : 0.005 0.052 1702 Dihedral : 8.407 100.575 1580 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % 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: -4.17 (0.20), residues: 1422 helix: -2.34 (0.21), residues: 514 sheet: -3.20 (0.43), residues: 108 loop : -3.10 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 303 HIS 0.010 0.002 HIS B 498 PHE 0.016 0.002 PHE B 456 TYR 0.023 0.002 TYR A 434 ARG 0.008 0.001 ARG A 162 *********************** 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 52 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.937 Fit side-chains REVERT: A 391 MET cc_start: 0.7662 (tmm) cc_final: 0.7406 (tmm) REVERT: B 391 MET cc_start: 0.7605 (tmm) cc_final: 0.7384 (tmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1848 time to fit residues: 15.6051 Evaluate side-chains 44 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.094129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068398 restraints weight = 31870.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067669 restraints weight = 23646.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.068680 restraints weight = 19019.293| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9436 Z= 0.144 Angle : 0.559 5.448 13012 Z= 0.289 Chirality : 0.043 0.167 1638 Planarity : 0.004 0.038 1702 Dihedral : 7.395 100.900 1580 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.21), residues: 1422 helix: -1.83 (0.22), residues: 510 sheet: -2.86 (0.48), residues: 86 loop : -2.82 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 297 HIS 0.004 0.001 HIS A 498 PHE 0.009 0.001 PHE B 333 TYR 0.012 0.001 TYR B 222 ARG 0.007 0.001 ARG B 162 *********************** 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 58 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.005 Fit side-chains REVERT: B 391 MET cc_start: 0.7403 (tmm) cc_final: 0.7180 (tmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1398 time to fit residues: 13.8479 Evaluate side-chains 46 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 79 optimal weight: 0.0020 chunk 64 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 72 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.096150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.071279 restraints weight = 31787.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068922 restraints weight = 24089.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069213 restraints weight = 25608.349| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9436 Z= 0.120 Angle : 0.546 6.589 13012 Z= 0.280 Chirality : 0.043 0.169 1638 Planarity : 0.004 0.043 1702 Dihedral : 6.979 102.479 1580 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % 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: -3.30 (0.21), residues: 1422 helix: -1.58 (0.22), residues: 522 sheet: -2.72 (0.48), residues: 90 loop : -2.64 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 529 HIS 0.003 0.001 HIS B 405 PHE 0.009 0.001 PHE B 275 TYR 0.011 0.001 TYR A 171 ARG 0.005 0.000 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 62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.998 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1196 time to fit residues: 13.5478 Evaluate side-chains 50 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 50 optimal weight: 40.0000 chunk 61 optimal weight: 50.0000 chunk 6 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 33 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS B 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.091725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070491 restraints weight = 32674.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.068171 restraints weight = 35153.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.068873 restraints weight = 38860.354| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9436 Z= 0.373 Angle : 0.690 6.374 13012 Z= 0.360 Chirality : 0.048 0.210 1638 Planarity : 0.005 0.044 1702 Dihedral : 8.097 96.600 1580 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -3.38 (0.22), residues: 1422 helix: -1.61 (0.23), residues: 518 sheet: -2.54 (0.48), residues: 88 loop : -2.73 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 529 HIS 0.010 0.002 HIS B 498 PHE 0.020 0.002 PHE A 456 TYR 0.031 0.003 TYR A 434 ARG 0.006 0.001 ARG A 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 54 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.962 Fit side-chains REVERT: A 391 MET cc_start: 0.7430 (tmm) cc_final: 0.7098 (tmm) REVERT: B 391 MET cc_start: 0.7399 (tmm) cc_final: 0.7096 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1477 time to fit residues: 13.5536 Evaluate side-chains 43 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 46 optimal weight: 40.0000 chunk 122 optimal weight: 30.0000 chunk 8 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.096286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.071228 restraints weight = 33590.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068909 restraints weight = 26043.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069329 restraints weight = 24975.131| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9436 Z= 0.136 Angle : 0.570 5.709 13012 Z= 0.292 Chirality : 0.043 0.225 1638 Planarity : 0.004 0.041 1702 Dihedral : 7.191 96.367 1580 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % 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: -3.07 (0.22), residues: 1422 helix: -1.31 (0.23), residues: 520 sheet: -2.69 (0.43), residues: 112 loop : -2.52 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 529 HIS 0.003 0.001 HIS B 498 PHE 0.010 0.001 PHE B 275 TYR 0.013 0.001 TYR B 434 ARG 0.003 0.000 ARG A 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 60 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1202 time to fit residues: 13.4478 Evaluate side-chains 49 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 141 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.095819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070221 restraints weight = 33129.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.068050 restraints weight = 24633.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068668 restraints weight = 23889.467| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9436 Z= 0.139 Angle : 0.556 5.672 13012 Z= 0.283 Chirality : 0.044 0.230 1638 Planarity : 0.004 0.043 1702 Dihedral : 7.002 97.215 1580 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -2.87 (0.22), residues: 1422 helix: -1.12 (0.23), residues: 522 sheet: -2.53 (0.44), residues: 112 loop : -2.43 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 529 HIS 0.003 0.001 HIS A 498 PHE 0.011 0.001 PHE A 275 TYR 0.012 0.001 TYR B 434 ARG 0.005 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 59 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.990 Fit side-chains REVERT: A 391 MET cc_start: 0.7443 (tmm) cc_final: 0.7200 (tmm) REVERT: B 391 MET cc_start: 0.7370 (tmm) cc_final: 0.7138 (tmm) REVERT: B 648 LEU cc_start: 0.8821 (tp) cc_final: 0.8454 (pt) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1156 time to fit residues: 12.6849 Evaluate side-chains 50 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 79 optimal weight: 0.3980 chunk 67 optimal weight: 20.0000 chunk 106 optimal weight: 0.0040 chunk 125 optimal weight: 8.9990 chunk 47 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 54 optimal weight: 8.9990 chunk 95 optimal weight: 0.0270 chunk 138 optimal weight: 40.0000 overall best weight: 0.1450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.098689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073378 restraints weight = 33264.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.071964 restraints weight = 27492.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072425 restraints weight = 20380.795| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9436 Z= 0.121 Angle : 0.546 5.628 13012 Z= 0.274 Chirality : 0.043 0.233 1638 Planarity : 0.004 0.046 1702 Dihedral : 6.657 98.461 1580 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -2.66 (0.22), residues: 1422 helix: -0.89 (0.23), residues: 524 sheet: -2.62 (0.42), residues: 124 loop : -2.29 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 529 HIS 0.008 0.001 HIS A 402 PHE 0.008 0.001 PHE B 392 TYR 0.011 0.001 TYR A 171 ARG 0.003 0.000 ARG A 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 62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.966 Fit side-chains REVERT: A 391 MET cc_start: 0.7367 (tmm) cc_final: 0.7089 (tmm) REVERT: B 648 LEU cc_start: 0.8669 (tp) cc_final: 0.8360 (pt) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1172 time to fit residues: 13.3981 Evaluate side-chains 48 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 52 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.092997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066727 restraints weight = 33786.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.064651 restraints weight = 27537.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065320 restraints weight = 26005.799| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9436 Z= 0.343 Angle : 0.662 5.641 13012 Z= 0.344 Chirality : 0.048 0.223 1638 Planarity : 0.004 0.040 1702 Dihedral : 7.670 96.400 1580 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % 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: -2.80 (0.22), residues: 1422 helix: -0.97 (0.24), residues: 506 sheet: -2.63 (0.43), residues: 124 loop : -2.40 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 486 HIS 0.009 0.002 HIS A 498 PHE 0.019 0.002 PHE B 456 TYR 0.027 0.002 TYR A 434 ARG 0.006 0.001 ARG A 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.06 seconds wall clock time: 50 minutes 33.61 seconds (3033.61 seconds total)