Starting phenix.real_space_refine on Thu Jul 2 17:51:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2026/7wi8_32527.map" } resolution = 4.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'GLU:plan': 31, 'ASP:plan': 27, 'ASN:plan1': 16, 'ARG:plan': 24, 'TYR:plan': 16, 'PHE:plan': 17, 'GLN:plan1': 14, 'HIS:plan': 3, 'TRP:plan': 6} 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 chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 3.28, per 1000 atoms: 0.35 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: 0.96 Conformation dependent library (CDL) restraints added in 404.1 milliseconds 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: 0.33 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: 1.25 Time building geometry restraints manager: 1.17 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 - 15.95: 4961 15.95 - 31.90: 427 31.90 - 47.85: 96 47.85 - 63.81: 18 63.81 - 79.76: 8 Dihedral angle restraints: 5510 sinusoidal: 1310 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 5507 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 9452 Z= 0.350 Angle : 1.030 15.571 13046 Z= 0.546 Chirality : 0.060 0.381 1638 Planarity : 0.006 0.063 1702 Dihedral : 13.842 79.757 2736 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG B 162 TYR 0.025 0.003 TYR A 434 PHE 0.021 0.002 PHE A 456 TRP 0.011 0.002 TRP B 210 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.35 ( 9436) covalent geometry : angle 1.00281 / 0.54 (13012) SS BOND : bond 0.00527 / 0.36 ( 14) SS BOND : angle 2.07234 / 1.23 ( 28) hydrogen bonds : bond 0.33435 / 22.78 ( 253) hydrogen bonds : angle 11.80821 / 8.24 ( 711) link_NAG-ASN : bond 0.01405 / 0.71 ( 2) link_NAG-ASN : angle 10.28461 / 5.22 ( 6) *********************** 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 : 0.254 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: 0.0562 time to fit residues: 5.5237 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 : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.0060 chunk 55 optimal weight: 20.0000 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.094896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070440 restraints weight = 31456.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068996 restraints weight = 25482.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.069500 restraints weight = 20000.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069656 restraints weight = 17778.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069695 restraints weight = 16721.904| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 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 = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9452 Z= 0.106 Angle : 0.629 10.454 13046 Z= 0.326 Chirality : 0.043 0.166 1638 Planarity : 0.004 0.045 1702 Dihedral : 6.527 56.055 1496 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.99 (0.18), residues: 1422 helix: -3.50 (0.16), residues: 496 sheet: -3.58 (0.38), residues: 108 loop : -3.25 (0.19), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.013 0.001 TYR A 434 PHE 0.013 0.001 PHE A 112 TRP 0.015 0.001 TRP B 297 HIS 0.001 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 9436) covalent geometry : angle 0.60513 / 0.32 (13012) SS BOND : bond 0.00485 / 0.29 ( 14) SS BOND : angle 1.89716 / 1.08 ( 28) hydrogen bonds : bond 0.03725 / 2.56 ( 253) hydrogen bonds : angle 6.48996 / 4.30 ( 711) link_NAG-ASN : bond 0.00752 / 0.38 ( 2) link_NAG-ASN : angle 6.93669 / 3.51 ( 6) *********************** 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 69 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.325 Fit side-chains REVERT: A 169 ILE cc_start: 0.8495 (mp) cc_final: 0.8282 (mm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0514 time to fit residues: 5.8019 Evaluate side-chains 45 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 33 optimal weight: 0.0980 chunk 59 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 52 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.091660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067493 restraints weight = 32136.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065015 restraints weight = 22805.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065804 restraints weight = 22616.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065858 restraints weight = 17576.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066641 restraints weight = 16404.720| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9452 Z= 0.195 Angle : 0.669 10.814 13046 Z= 0.347 Chirality : 0.046 0.155 1638 Planarity : 0.005 0.046 1702 Dihedral : 6.618 51.168 1496 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.59 (0.19), residues: 1422 helix: -2.78 (0.19), residues: 514 sheet: -3.56 (0.39), residues: 108 loop : -3.25 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 644 TYR 0.023 0.002 TYR A 434 PHE 0.017 0.002 PHE A 456 TRP 0.044 0.002 TRP B 303 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 9436) covalent geometry : angle 0.64853 / 0.34 (13012) SS BOND : bond 0.00688 / 0.45 ( 14) SS BOND : angle 1.13079 / 0.71 ( 28) hydrogen bonds : bond 0.03691 / 2.56 ( 253) hydrogen bonds : angle 6.12298 / 4.05 ( 711) link_NAG-ASN : bond 0.01033 / 0.52 ( 2) link_NAG-ASN : angle 7.37063 / 3.75 ( 6) *********************** 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 62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0722 time to fit residues: 6.5352 Evaluate side-chains 47 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 2 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 0.0980 chunk 115 optimal weight: 8.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 GLN B 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.096030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.070788 restraints weight = 31170.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069863 restraints weight = 27239.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.070455 restraints weight = 22421.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070864 restraints weight = 17187.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070931 restraints weight = 15027.556| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9452 Z= 0.095 Angle : 0.583 9.877 13046 Z= 0.297 Chirality : 0.042 0.160 1638 Planarity : 0.004 0.040 1702 Dihedral : 5.885 54.445 1496 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.20), residues: 1422 helix: -2.14 (0.21), residues: 494 sheet: -3.28 (0.40), residues: 112 loop : -2.96 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 644 TYR 0.012 0.001 TYR A 398 PHE 0.008 0.001 PHE B 333 TRP 0.012 0.001 TRP A 297 HIS 0.001 0.000 HIS A 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 9436) covalent geometry : angle 0.56186 / 0.29 (13012) SS BOND : bond 0.00286 / 0.18 ( 14) SS BOND : angle 1.68250 / 0.96 ( 28) hydrogen bonds : bond 0.02669 / 1.88 ( 253) hydrogen bonds : angle 5.58308 / 3.65 ( 711) link_NAG-ASN : bond 0.00957 / 0.48 ( 2) link_NAG-ASN : angle 6.39003 / 3.20 ( 6) *********************** 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 64 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.364 Fit side-chains REVERT: A 391 MET cc_start: 0.7274 (tmm) cc_final: 0.7071 (tmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0702 time to fit residues: 6.9986 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 : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 27 optimal weight: 0.0270 chunk 143 optimal weight: 30.0000 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3745 r_free = 0.3745 target = 0.092760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068406 restraints weight = 31467.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066834 restraints weight = 23195.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.067251 restraints weight = 22815.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067622 restraints weight = 18894.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.067639 restraints weight = 16296.838| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9452 Z= 0.156 Angle : 0.633 10.231 13046 Z= 0.324 Chirality : 0.045 0.159 1638 Planarity : 0.004 0.038 1702 Dihedral : 6.038 50.531 1496 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.21), residues: 1422 helix: -1.99 (0.22), residues: 514 sheet: -3.19 (0.42), residues: 108 loop : -2.80 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 644 TYR 0.019 0.002 TYR B 434 PHE 0.014 0.002 PHE A 275 TRP 0.011 0.001 TRP B 303 HIS 0.007 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 ( 9436) covalent geometry : angle 0.61203 / 0.32 (13012) SS BOND : bond 0.00533 / 0.35 ( 14) SS BOND : angle 1.63966 / 1.01 ( 28) hydrogen bonds : bond 0.02864 / 2.00 ( 253) hydrogen bonds : angle 5.55982 / 3.66 ( 711) link_NAG-ASN : bond 0.01058 / 0.53 ( 2) link_NAG-ASN : angle 6.87777 / 3.49 ( 6) *********************** 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 57 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.307 Fit side-chains REVERT: B 391 MET cc_start: 0.7431 (tmm) cc_final: 0.7170 (tmm) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.0782 time to fit residues: 6.9031 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 : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.093131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067122 restraints weight = 32555.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066354 restraints weight = 23224.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.066707 restraints weight = 20308.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.066661 restraints weight = 16933.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066736 restraints weight = 16567.351| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9452 Z= 0.141 Angle : 0.614 10.440 13046 Z= 0.312 Chirality : 0.044 0.150 1638 Planarity : 0.004 0.038 1702 Dihedral : 5.940 49.202 1496 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.21), residues: 1422 helix: -1.72 (0.22), residues: 516 sheet: -3.13 (0.40), residues: 112 loop : -2.74 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 644 TYR 0.017 0.002 TYR B 434 PHE 0.012 0.001 PHE A 275 TRP 0.010 0.001 TRP B 297 HIS 0.006 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9436) covalent geometry : angle 0.59504 / 0.31 (13012) SS BOND : bond 0.00252 / 0.16 ( 14) SS BOND : angle 0.94476 / 0.59 ( 28) hydrogen bonds : bond 0.02735 / 1.91 ( 253) hydrogen bonds : angle 5.46989 / 3.58 ( 711) link_NAG-ASN : bond 0.01050 / 0.53 ( 2) link_NAG-ASN : angle 6.86524 / 3.46 ( 6) *********************** 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 54 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0507 time to fit residues: 5.0296 Evaluate side-chains 47 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 26 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.094369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073337 restraints weight = 33872.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.070649 restraints weight = 36123.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071548 restraints weight = 37252.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.071575 restraints weight = 22904.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.072680 restraints weight = 20062.708| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9452 Z= 0.155 Angle : 0.635 10.543 13046 Z= 0.323 Chirality : 0.045 0.178 1638 Planarity : 0.004 0.037 1702 Dihedral : 6.016 48.112 1496 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.21), residues: 1422 helix: -1.70 (0.22), residues: 534 sheet: -2.97 (0.42), residues: 112 loop : -2.63 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.021 0.002 TYR A 434 PHE 0.014 0.001 PHE A 456 TRP 0.015 0.001 TRP A 529 HIS 0.007 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9436) covalent geometry : angle 0.61481 / 0.32 (13012) SS BOND : bond 0.00253 / 0.17 ( 14) SS BOND : angle 1.41370 / 0.84 ( 28) hydrogen bonds : bond 0.02761 / 1.93 ( 253) hydrogen bonds : angle 5.44926 / 3.56 ( 711) link_NAG-ASN : bond 0.01097 / 0.55 ( 2) link_NAG-ASN : angle 6.98287 / 3.53 ( 6) *********************** 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 58 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.365 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0609 time to fit residues: 5.9143 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 : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.0060 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 chunk 68 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.095007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073113 restraints weight = 33304.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070888 restraints weight = 33528.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071576 restraints weight = 36252.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071614 restraints weight = 23849.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072385 restraints weight = 20394.081| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9452 Z= 0.120 Angle : 0.612 10.293 13046 Z= 0.309 Chirality : 0.044 0.222 1638 Planarity : 0.004 0.039 1702 Dihedral : 5.760 49.546 1496 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.22), residues: 1422 helix: -1.46 (0.23), residues: 526 sheet: -2.86 (0.42), residues: 112 loop : -2.55 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.020 0.002 TYR B 434 PHE 0.011 0.001 PHE B 456 TRP 0.011 0.001 TRP A 529 HIS 0.005 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9436) covalent geometry : angle 0.59355 / 0.30 (13012) SS BOND : bond 0.00214 / 0.14 ( 14) SS BOND : angle 1.14639 / 0.71 ( 28) hydrogen bonds : bond 0.02544 / 1.79 ( 253) hydrogen bonds : angle 5.31832 / 3.46 ( 711) link_NAG-ASN : bond 0.01054 / 0.53 ( 2) link_NAG-ASN : angle 6.71511 / 3.39 ( 6) *********************** 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 53 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.381 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0464 time to fit residues: 4.6514 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 : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 30.0000 chunk 19 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.093772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067475 restraints weight = 33613.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.066479 restraints weight = 25211.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067284 restraints weight = 21090.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.067108 restraints weight = 17723.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.067288 restraints weight = 17634.250| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9452 Z= 0.150 Angle : 0.636 10.451 13046 Z= 0.322 Chirality : 0.046 0.228 1638 Planarity : 0.004 0.037 1702 Dihedral : 5.846 46.450 1496 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.22), residues: 1422 helix: -1.29 (0.23), residues: 514 sheet: -2.81 (0.42), residues: 112 loop : -2.54 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 277 TYR 0.023 0.002 TYR A 434 PHE 0.014 0.001 PHE B 456 TRP 0.016 0.001 TRP B 529 HIS 0.007 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9436) covalent geometry : angle 0.61795 / 0.32 (13012) SS BOND : bond 0.00188 / 0.13 ( 14) SS BOND : angle 0.95863 / 0.60 ( 28) hydrogen bonds : bond 0.02764 / 1.94 ( 253) hydrogen bonds : angle 5.35829 / 3.49 ( 711) link_NAG-ASN : bond 0.01106 / 0.55 ( 2) link_NAG-ASN : angle 6.91798 / 3.50 ( 6) *********************** 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 56 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.391 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0445 time to fit residues: 4.4701 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 : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 68 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 40.0000 chunk 139 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.092881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071002 restraints weight = 33684.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068419 restraints weight = 34020.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.069302 restraints weight = 36859.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.069463 restraints weight = 23045.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070218 restraints weight = 20043.734| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9452 Z= 0.184 Angle : 0.677 11.266 13046 Z= 0.342 Chirality : 0.047 0.229 1638 Planarity : 0.004 0.036 1702 Dihedral : 5.992 37.857 1496 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.22), residues: 1422 helix: -1.47 (0.23), residues: 532 sheet: -2.67 (0.44), residues: 108 loop : -2.52 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 277 TYR 0.024 0.002 TYR A 434 PHE 0.014 0.002 PHE A 456 TRP 0.018 0.002 TRP A 529 HIS 0.008 0.002 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 9436) covalent geometry : angle 0.65638 / 0.34 (13012) SS BOND : bond 0.00200 / 0.14 ( 14) SS BOND : angle 1.09853 / 0.69 ( 28) hydrogen bonds : bond 0.02958 / 2.07 ( 253) hydrogen bonds : angle 5.55229 / 3.64 ( 711) link_NAG-ASN : bond 0.01220 / 0.61 ( 2) link_NAG-ASN : angle 7.48541 / 3.79 ( 6) ********************** 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 55 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.276 Fit side-chains REVERT: A 391 MET cc_start: 0.7196 (tmm) cc_final: 0.6925 (tmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0507 time to fit residues: 5.0259 Evaluate side-chains 47 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 45 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 50 optimal weight: 40.0000 chunk 20 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 0.0020 chunk 74 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072909 restraints weight = 33222.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070839 restraints weight = 32414.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.071524 restraints weight = 34314.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.071777 restraints weight = 21684.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072444 restraints weight = 18791.613| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9452 Z= 0.120 Angle : 0.620 10.677 13046 Z= 0.313 Chirality : 0.044 0.229 1638 Planarity : 0.004 0.038 1702 Dihedral : 5.514 39.325 1496 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.22), residues: 1422 helix: -1.18 (0.24), residues: 514 sheet: -2.61 (0.44), residues: 112 loop : -2.45 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.017 0.002 TYR A 434 PHE 0.010 0.001 PHE A 456 TRP 0.019 0.001 TRP A 529 HIS 0.004 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9436) covalent geometry : angle 0.59757 / 0.31 (13012) SS BOND : bond 0.00489 / 0.31 ( 14) SS BOND : angle 1.68748 / 1.03 ( 28) hydrogen bonds : bond 0.02513 / 1.77 ( 253) hydrogen bonds : angle 5.30015 / 3.43 ( 711) link_NAG-ASN : bond 0.01121 / 0.56 ( 2) link_NAG-ASN : angle 6.95156 / 3.51 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.61 seconds wall clock time: 22 minutes 26.58 seconds (1346.58 seconds total)