Starting phenix.real_space_refine on Sun Jul 27 17:23:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wi8_32527/07_2025/7wi8_32527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi8_32527/07_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_32527/07_2025/7wi8_32527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2025/7wi8_32527.map" model { file = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_2025/7wi8_32527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi8_32527/07_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-5711/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: 9.34, per 1000 atoms: 1.01 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: 2.43 Conformation dependent library (CDL) restraints added in 1.3 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: 1.46 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: 2.78 Time building geometry restraints manager: 2.81 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: 0.06 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.920 ------------------------------------------------------------------------------- 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 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 : 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01405 ( 2) link_NAG-ASN : angle 10.28461 ( 6) hydrogen bonds : bond 0.33435 ( 253) hydrogen bonds : angle 11.80821 ( 711) SS BOND : bond 0.00527 ( 14) SS BOND : angle 2.07234 ( 28) covalent geometry : bond 0.00766 ( 9436) covalent geometry : angle 1.00281 (13012) *********************** 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 : 1.104 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: 0.1567 time to fit residues: 15.6794 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 : 1.054 ------------------------------------------------------------------------------- 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: 3.9990 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 9452 Z= 0.108 Angle : 0.630 10.488 13046 Z= 0.325 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00705 ( 2) link_NAG-ASN : angle 6.99233 ( 6) hydrogen bonds : bond 0.03648 ( 253) hydrogen bonds : angle 6.44226 ( 711) SS BOND : bond 0.00337 ( 14) SS BOND : angle 1.91429 ( 28) covalent geometry : bond 0.00219 ( 9436) covalent geometry : angle 0.60641 (13012) *********************** 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 : 1.060 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: 0.1469 time to fit residues: 17.2398 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 : 1.112 ------------------------------------------------------------------------------- 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: 0.0870 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: 0.3980 chunk 100 optimal weight: 0.2980 overall best weight: 1.7570 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.093113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.068081 restraints weight = 32191.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.066222 restraints weight = 23339.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.067100 restraints weight = 23234.986| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9452 Z= 0.143 Angle : 0.623 10.407 13046 Z= 0.321 Chirality : 0.044 0.151 1638 Planarity : 0.004 0.037 1702 Dihedral : 8.611 101.004 1580 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % 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: -2.64 (0.20), residues: 482 sheet: -3.40 (0.40), residues: 108 loop : -3.15 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 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 644 Details of bonding type rmsd link_NAG-ASN : bond 0.00994 ( 2) link_NAG-ASN : angle 7.12596 ( 6) hydrogen bonds : bond 0.03358 ( 253) hydrogen bonds : angle 5.91059 ( 711) SS BOND : bond 0.00366 ( 14) SS BOND : angle 0.89007 ( 28) covalent geometry : bond 0.00320 ( 9436) covalent geometry : angle 0.60291 (13012) *********************** 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 63 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2968 time to fit residues: 28.4436 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 : 1.319 ------------------------------------------------------------------------------- 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: 0.2980 chunk 50 optimal weight: 40.0000 chunk 91 optimal weight: 0.4980 chunk 113 optimal weight: 20.0000 chunk 61 optimal weight: 50.0000 chunk 129 optimal weight: 9.9990 chunk 79 optimal weight: 0.0050 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.094385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.073982 restraints weight = 31204.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072711 restraints weight = 32604.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.073323 restraints weight = 34010.904| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9452 Z= 0.103 Angle : 0.592 9.896 13046 Z= 0.301 Chirality : 0.043 0.164 1638 Planarity : 0.004 0.037 1702 Dihedral : 8.170 101.353 1580 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % 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 (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: -3.95 (0.20), residues: 1422 helix: -2.13 (0.21), residues: 494 sheet: -3.16 (0.42), residues: 108 loop : -2.97 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS A 498 PHE 0.010 0.001 PHE A 275 TYR 0.012 0.001 TYR B 434 ARG 0.007 0.001 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00991 ( 2) link_NAG-ASN : angle 6.62114 ( 6) hydrogen bonds : bond 0.02732 ( 253) hydrogen bonds : angle 5.66336 ( 711) SS BOND : bond 0.00240 ( 14) SS BOND : angle 1.59292 ( 28) covalent geometry : bond 0.00228 ( 9436) covalent geometry : angle 0.57087 (13012) *********************** 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 59 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.308 Fit side-chains REVERT: A 391 MET cc_start: 0.7160 (tmm) cc_final: 0.6895 (tmm) REVERT: B 391 MET cc_start: 0.7110 (tmm) cc_final: 0.6873 (tmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1652 time to fit residues: 15.7636 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 : 1.068 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 402 HIS B 402 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.072703 restraints weight = 31527.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071704 restraints weight = 33344.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.072042 restraints weight = 30501.378| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9452 Z= 0.140 Angle : 0.617 10.229 13046 Z= 0.312 Chirality : 0.045 0.161 1638 Planarity : 0.004 0.036 1702 Dihedral : 7.852 101.016 1580 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: -3.70 (0.21), residues: 1422 helix: -1.89 (0.22), residues: 508 sheet: -3.09 (0.42), residues: 108 loop : -2.83 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 529 HIS 0.007 0.001 HIS B 498 PHE 0.012 0.001 PHE A 456 TYR 0.018 0.002 TYR A 434 ARG 0.006 0.001 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.01054 ( 2) link_NAG-ASN : angle 6.93650 ( 6) hydrogen bonds : bond 0.02785 ( 253) hydrogen bonds : angle 5.52249 ( 711) SS BOND : bond 0.00229 ( 14) SS BOND : angle 1.26045 ( 28) covalent geometry : bond 0.00316 ( 9436) covalent geometry : angle 0.59703 (13012) *********************** 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 56 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.044 Fit side-chains REVERT: A 391 MET cc_start: 0.7395 (tmm) cc_final: 0.7062 (tmm) REVERT: B 391 MET cc_start: 0.7360 (tmm) cc_final: 0.7051 (tmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1472 time to fit residues: 14.4546 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 : 1.061 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.093298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.068001 restraints weight = 31554.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.066036 restraints weight = 23411.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066635 restraints weight = 22769.805| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.003 0.040 9452 Z= 0.129 Angle : 0.596 10.115 13046 Z= 0.304 Chirality : 0.044 0.153 1638 Planarity : 0.004 0.037 1702 Dihedral : 7.476 100.250 1580 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.87 % Favored : 87.13 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.21), residues: 1422 helix: -1.66 (0.22), residues: 512 sheet: -3.05 (0.41), residues: 112 loop : -2.71 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 529 HIS 0.006 0.001 HIS B 498 PHE 0.011 0.001 PHE A 456 TYR 0.015 0.002 TYR A 434 ARG 0.005 0.001 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.01020 ( 2) link_NAG-ASN : angle 6.75385 ( 6) hydrogen bonds : bond 0.02587 ( 253) hydrogen bonds : angle 5.39143 ( 711) SS BOND : bond 0.00196 ( 14) SS BOND : angle 1.34325 ( 28) covalent geometry : bond 0.00291 ( 9436) covalent geometry : angle 0.57533 (13012) *********************** 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 51 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1179 time to fit residues: 11.3428 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 : 1.023 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.091337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070925 restraints weight = 32099.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069224 restraints weight = 35070.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069653 restraints weight = 35659.554| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9452 Z= 0.201 Angle : 0.671 10.933 13046 Z= 0.343 Chirality : 0.047 0.211 1638 Planarity : 0.004 0.038 1702 Dihedral : 7.970 97.077 1580 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.21), residues: 1422 helix: -1.61 (0.23), residues: 518 sheet: -2.91 (0.43), residues: 108 loop : -2.70 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 529 HIS 0.009 0.002 HIS B 498 PHE 0.015 0.002 PHE A 456 TYR 0.028 0.002 TYR B 434 ARG 0.005 0.001 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.01124 ( 2) link_NAG-ASN : angle 7.46102 ( 6) hydrogen bonds : bond 0.03036 ( 253) hydrogen bonds : angle 5.57626 ( 711) SS BOND : bond 0.00293 ( 14) SS BOND : angle 1.49152 ( 28) covalent geometry : bond 0.00460 ( 9436) covalent geometry : angle 0.64847 (13012) *********************** 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 51 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.977 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1183 time to fit residues: 11.3952 Evaluate side-chains 42 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 122 optimal weight: 40.0000 chunk 8 optimal weight: 0.7980 overall best weight: 1.3662 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.095319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074192 restraints weight = 33769.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072012 restraints weight = 35284.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072520 restraints weight = 37391.870| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2910 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= 0.118 Angle : 0.608 10.583 13046 Z= 0.309 Chirality : 0.044 0.223 1638 Planarity : 0.004 0.038 1702 Dihedral : 7.485 96.428 1580 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1422 helix: -1.40 (0.23), residues: 518 sheet: -2.79 (0.42), residues: 112 loop : -2.52 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 529 HIS 0.005 0.001 HIS A 498 PHE 0.012 0.001 PHE B 456 TYR 0.019 0.002 TYR B 434 ARG 0.005 0.001 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.01032 ( 2) link_NAG-ASN : angle 6.93241 ( 6) hydrogen bonds : bond 0.02592 ( 253) hydrogen bonds : angle 5.37687 ( 711) SS BOND : bond 0.00246 ( 14) SS BOND : angle 1.12472 ( 28) covalent geometry : bond 0.00263 ( 9436) covalent geometry : angle 0.58835 (13012) *********************** 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 : 1.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1446 time to fit residues: 14.6131 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 : 1.055 ------------------------------------------------------------------------------- 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: 0.0270 chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 100 optimal weight: 0.0770 chunk 39 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 141 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.096238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070281 restraints weight = 33069.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068759 restraints weight = 26947.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069414 restraints weight = 21023.083| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9452 Z= 0.087 Angle : 0.577 9.740 13046 Z= 0.290 Chirality : 0.043 0.216 1638 Planarity : 0.004 0.042 1702 Dihedral : 6.981 97.132 1580 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: -2.93 (0.22), residues: 1422 helix: -1.21 (0.23), residues: 520 sheet: -2.63 (0.43), residues: 112 loop : -2.41 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 529 HIS 0.002 0.000 HIS B 498 PHE 0.007 0.001 PHE A 333 TYR 0.012 0.001 TYR B 434 ARG 0.004 0.000 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00911 ( 2) link_NAG-ASN : angle 6.40395 ( 6) hydrogen bonds : bond 0.02245 ( 253) hydrogen bonds : angle 5.17121 ( 711) SS BOND : bond 0.00247 ( 14) SS BOND : angle 0.75948 ( 28) covalent geometry : bond 0.00181 ( 9436) covalent geometry : angle 0.56020 (13012) *********************** 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 61 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.448 Fit side-chains REVERT: B 648 LEU cc_start: 0.8737 (tp) cc_final: 0.8401 (pt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1334 time to fit residues: 15.2580 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 : 0.899 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 47 optimal weight: 0.0040 chunk 112 optimal weight: 0.0270 chunk 48 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 95 optimal weight: 0.0040 chunk 138 optimal weight: 40.0000 overall best weight: 1.5264 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.095648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069655 restraints weight = 33551.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068269 restraints weight = 24999.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068733 restraints weight = 21819.153| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3148 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= 0.122 Angle : 0.595 9.673 13046 Z= 0.301 Chirality : 0.045 0.224 1638 Planarity : 0.004 0.040 1702 Dihedral : 7.257 96.970 1580 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % 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 (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: -1.11 (0.24), residues: 518 sheet: -2.68 (0.43), residues: 112 loop : -2.39 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 529 HIS 0.006 0.001 HIS B 498 PHE 0.012 0.001 PHE B 275 TYR 0.018 0.002 TYR B 434 ARG 0.006 0.001 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.01022 ( 2) link_NAG-ASN : angle 6.56777 ( 6) hydrogen bonds : bond 0.02489 ( 253) hydrogen bonds : angle 5.14271 ( 711) SS BOND : bond 0.00276 ( 14) SS BOND : angle 0.67511 ( 28) covalent geometry : bond 0.00272 ( 9436) covalent geometry : angle 0.57799 (13012) ********************** 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 57 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.002 Fit side-chains REVERT: B 648 LEU cc_start: 0.8750 (tp) cc_final: 0.8416 (pt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1553 time to fit residues: 15.8193 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 : 1.331 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 143 optimal weight: 0.0470 chunk 67 optimal weight: 20.0000 chunk 52 optimal weight: 0.0570 chunk 92 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.095740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070507 restraints weight = 33210.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067870 restraints weight = 25549.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068491 restraints weight = 24961.269| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9452 Z= 0.092 Angle : 0.567 9.478 13046 Z= 0.285 Chirality : 0.043 0.221 1638 Planarity : 0.004 0.041 1702 Dihedral : 6.998 96.587 1580 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % 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: -2.74 (0.22), residues: 1422 helix: -1.00 (0.24), residues: 518 sheet: -2.56 (0.43), residues: 112 loop : -2.33 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 529 HIS 0.003 0.001 HIS B 498 PHE 0.009 0.001 PHE B 275 TYR 0.013 0.001 TYR B 434 ARG 0.004 0.001 ARG A 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00928 ( 2) link_NAG-ASN : angle 6.29854 ( 6) hydrogen bonds : bond 0.02235 ( 253) hydrogen bonds : angle 5.04376 ( 711) SS BOND : bond 0.00183 ( 14) SS BOND : angle 0.66177 ( 28) covalent geometry : bond 0.00201 ( 9436) covalent geometry : angle 0.55004 (13012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2883.85 seconds wall clock time: 52 minutes 25.12 seconds (3145.12 seconds total)