Starting phenix.real_space_refine on Sat Sep 12 06:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.map" model { file = "/net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p07_20226/09_2026/6p07_20226.cif" } resolution = 3.2 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= 0.002 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 28 5.16 5 C 8756 2.51 5 N 2481 2.21 5 O 2781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14072 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2102 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 261} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2344 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2333 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 13, 'TRANS': 287} Chain: "D" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2347 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain: "E" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2347 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain: "F" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2244 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 286} Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 136 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'TRANS': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 59 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Conformer: "B" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1'AATP F 801 " occ=0.50 ... (29 atoms not shown) pdb=" PG AATP F 801 " occ=0.50 residue: pdb=" C1'BADP F 802 " occ=0.50 ... (25 atoms not shown) pdb=" PB BADP F 802 " occ=0.50 Time building chain proxies: 3.06, per 1000 atoms: 0.22 Number of scatterers: 14072 At special positions: 0 Unit cell: (101.2, 133.4, 138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 20 15.00 Mg 6 11.99 O 2781 8.00 N 2481 7.00 C 8756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 627.9 milliseconds 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 9 sheets defined 54.2% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 463 through 472 removed outlier: 4.010A pdb=" N ILE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'A' and resid 528 through 541 removed outlier: 3.524A pdb=" N CYS A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 541 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 553 removed outlier: 4.010A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 553' Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'A' and resid 596 through 612 removed outlier: 3.896A pdb=" N GLY A 612 " --> pdb=" O VAL A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.569A pdb=" N GLU A 633 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 634 " --> pdb=" O PRO A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 635 through 640 removed outlier: 3.505A pdb=" N ARG A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 Processing helix chain 'A' and resid 672 through 683 removed outlier: 3.616A pdb=" N ARG A 677 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 removed outlier: 3.618A pdb=" N LEU A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 708 through 713 removed outlier: 3.891A pdb=" N LYS A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 730 Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 739 through 750 removed outlier: 3.776A pdb=" N SER A 745 " --> pdb=" O GLN A 741 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 472 removed outlier: 4.096A pdb=" N VAL B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 499 Processing helix chain 'B' and resid 499 through 505 removed outlier: 3.573A pdb=" N SER B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.732A pdb=" N ALA B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.765A pdb=" N SER B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 552 " --> pdb=" O ALA B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 552' Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.644A pdb=" N LEU B 563 " --> pdb=" O ASP B 559 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 565 " --> pdb=" O GLU B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 612 removed outlier: 3.574A pdb=" N ARG B 600 " --> pdb=" O HIS B 596 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY B 612 " --> pdb=" O VAL B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.575A pdb=" N ARG B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 668 Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.558A pdb=" N LEU B 676 " --> pdb=" O ASP B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 705 removed outlier: 3.526A pdb=" N LEU B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Proline residue: B 702 - end of helix removed outlier: 3.637A pdb=" N GLU B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 712 Processing helix chain 'B' and resid 723 through 732 removed outlier: 3.609A pdb=" N PHE B 727 " --> pdb=" O THR B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 753 removed outlier: 3.555A pdb=" N LEU B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 752 " --> pdb=" O LYS B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 472 removed outlier: 3.764A pdb=" N VAL C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 472 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 529 through 540 Processing helix chain 'C' and resid 561 through 574 Processing helix chain 'C' and resid 596 through 611 removed outlier: 3.546A pdb=" N ARG C 600 " --> pdb=" O HIS C 596 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'C' and resid 652 through 664 Processing helix chain 'C' and resid 672 through 683 removed outlier: 3.673A pdb=" N LEU C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 705 Proline residue: C 702 - end of helix Processing helix chain 'C' and resid 723 through 732 removed outlier: 3.691A pdb=" N PHE C 727 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 732 " --> pdb=" O HIS C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 removed outlier: 3.634A pdb=" N TYR C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 754 Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 481 through 485 Processing helix chain 'D' and resid 488 through 499 Processing helix chain 'D' and resid 499 through 505 removed outlier: 3.738A pdb=" N SER D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 538 Processing helix chain 'D' and resid 559 through 574 Processing helix chain 'D' and resid 596 through 611 removed outlier: 4.277A pdb=" N ASP D 611 " --> pdb=" O LEU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 620 removed outlier: 4.167A pdb=" N ASP D 620 " --> pdb=" O PRO D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 removed outlier: 3.812A pdb=" N GLU D 633 " --> pdb=" O ARG D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 652 through 666 Processing helix chain 'D' and resid 672 through 683 removed outlier: 3.559A pdb=" N LEU D 676 " --> pdb=" O ASP D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 705 Proline residue: D 702 - end of helix removed outlier: 3.598A pdb=" N GLU D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 removed outlier: 3.586A pdb=" N PHE D 727 " --> pdb=" O THR D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 751 removed outlier: 3.877A pdb=" N LEU D 743 " --> pdb=" O ALA D 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 472 removed outlier: 3.715A pdb=" N GLU E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 485 Processing helix chain 'E' and resid 488 through 499 Processing helix chain 'E' and resid 500 through 504 Processing helix chain 'E' and resid 510 through 514 Processing helix chain 'E' and resid 529 through 539 Processing helix chain 'E' and resid 560 through 574 removed outlier: 3.664A pdb=" N VAL E 564 " --> pdb=" O GLY E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 587 Processing helix chain 'E' and resid 596 through 611 removed outlier: 3.811A pdb=" N ARG E 600 " --> pdb=" O HIS E 596 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP E 611 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 620 removed outlier: 3.605A pdb=" N ASP E 620 " --> pdb=" O PRO E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 635 through 641 removed outlier: 3.978A pdb=" N ARG E 640 " --> pdb=" O GLU E 636 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG E 641 " --> pdb=" O ALA E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 664 Processing helix chain 'E' and resid 673 through 683 Processing helix chain 'E' and resid 687 through 701 Processing helix chain 'E' and resid 702 through 706 Processing helix chain 'E' and resid 708 through 712 removed outlier: 3.604A pdb=" N VAL E 711 " --> pdb=" O VAL E 708 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 732 removed outlier: 3.674A pdb=" N LYS E 732 " --> pdb=" O HIS E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 741 No H-bonds generated for 'chain 'E' and resid 739 through 741' Processing helix chain 'E' and resid 742 through 754 removed outlier: 3.865A pdb=" N TYR E 746 " --> pdb=" O SER E 742 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP E 752 " --> pdb=" O LYS E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 472 removed outlier: 3.730A pdb=" N VAL F 466 " --> pdb=" O GLU F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 485 Processing helix chain 'F' and resid 488 through 499 Processing helix chain 'F' and resid 530 through 540 Processing helix chain 'F' and resid 559 through 574 Processing helix chain 'F' and resid 583 through 588 removed outlier: 4.176A pdb=" N LEU F 587 " --> pdb=" O GLN F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 612 removed outlier: 3.560A pdb=" N ASP F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY F 612 " --> pdb=" O VAL F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 635 through 642 removed outlier: 3.560A pdb=" N ARG F 641 " --> pdb=" O ALA F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 665 Processing helix chain 'F' and resid 666 through 668 No H-bonds generated for 'chain 'F' and resid 666 through 668' Processing helix chain 'F' and resid 672 through 675 Processing helix chain 'F' and resid 676 through 683 removed outlier: 3.673A pdb=" N ALA F 680 " --> pdb=" O LEU F 676 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR F 683 " --> pdb=" O LEU F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 707 removed outlier: 3.588A pdb=" N ALA F 693 " --> pdb=" O SER F 689 " (cutoff:3.500A) Proline residue: F 702 - end of helix Processing helix chain 'F' and resid 739 through 753 removed outlier: 3.509A pdb=" N LEU F 743 " --> pdb=" O ALA F 739 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 624 through 625 removed outlier: 3.982A pdb=" N LYS A 644 " --> pdb=" O GLY A 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AA3, first strand: chain 'B' and resid 543 through 547 removed outlier: 5.791A pdb=" N THR B 543 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B 580 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 545 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASP B 582 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 547 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU B 625 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 579 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ALA B 627 " --> pdb=" O ILE B 579 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE B 581 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 519 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 518 " --> pdb=" O LYS B 644 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N VAL B 646 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 520 " --> pdb=" O VAL B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.391A pdb=" N LEU C 520 " --> pdb=" O VAL C 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 543 through 547 removed outlier: 3.697A pdb=" N ALA C 627 " --> pdb=" O ILE C 581 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 474 removed outlier: 4.551A pdb=" N PHE D 544 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR D 543 " --> pdb=" O ILE D 578 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE D 580 " --> pdb=" O THR D 543 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU D 545 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP D 582 " --> pdb=" O LEU D 545 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE D 547 " --> pdb=" O ASP D 582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 519 through 522 Processing sheet with id=AA8, first strand: chain 'E' and resid 543 through 547 removed outlier: 8.010A pdb=" N LEU E 625 " --> pdb=" O SER E 577 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE E 579 " --> pdb=" O LEU E 625 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ALA E 627 " --> pdb=" O ILE E 579 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE E 581 " --> pdb=" O ALA E 627 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 520 " --> pdb=" O VAL E 646 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 544 through 547 removed outlier: 6.017A pdb=" N LEU F 545 " --> pdb=" O PHE F 580 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE F 579 " --> pdb=" O LEU F 625 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA F 627 " --> pdb=" O ILE F 579 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE F 581 " --> pdb=" O ALA F 627 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 520 " --> pdb=" O LYS F 644 " (cutoff:3.500A) 571 hydrogen bonds defined for protein. 1614 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: 1.93 Time building geometry restraints manager: 1.45 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: 4680 1.34 - 1.45: 1647 1.45 - 1.57: 7861 1.57 - 1.69: 33 1.69 - 1.81: 45 Bond restraints: 14266 Sorted by residual: bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 AATP F 801 " pdb=" C5 AATP F 801 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP B 801 " pdb=" C5 ATP B 801 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.08e+01 ... (remaining 14261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 19259 5.04 - 10.08: 74 10.08 - 15.13: 0 15.13 - 20.17: 3 20.17 - 25.21: 9 Bond angle restraints: 19345 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 114.66 25.21 1.00e+00 1.00e+00 6.36e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 112.43 24.40 1.00e+00 1.00e+00 5.95e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 116.84 23.03 1.00e+00 1.00e+00 5.30e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 117.99 21.88 1.00e+00 1.00e+00 4.79e+02 angle pdb=" PA ATP E 801 " pdb=" O3A ATP E 801 " pdb=" PB ATP E 801 " ideal model delta sigma weight residual 136.83 115.38 21.45 1.00e+00 1.00e+00 4.60e+02 ... (remaining 19340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.05: 8495 20.05 - 40.10: 229 40.10 - 60.15: 15 60.15 - 80.21: 4 80.21 - 100.26: 1 Dihedral angle restraints: 8744 sinusoidal: 3547 harmonic: 5197 Sorted by residual: dihedral pdb=" CA ASN E 527 " pdb=" C ASN E 527 " pdb=" N GLY E 528 " pdb=" CA GLY E 528 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" O1BBADP F 802 " pdb=" O3ABADP F 802 " pdb=" PB BADP F 802 " pdb=" PA BADP F 802 " ideal model delta sinusoidal sigma weight residual -60.00 -160.26 100.26 1 2.00e+01 2.50e-03 2.83e+01 dihedral pdb=" CA MET B 574 " pdb=" C MET B 574 " pdb=" N GLN B 575 " pdb=" CA GLN B 575 " ideal model delta harmonic sigma weight residual 180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 8741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1380 0.036 - 0.072: 598 0.072 - 0.108: 205 0.108 - 0.144: 63 0.144 - 0.180: 8 Chirality restraints: 2254 Sorted by residual: chirality pdb=" C2' ATP D 801 " pdb=" C1' ATP D 801 " pdb=" C3' ATP D 801 " pdb=" O2' ATP D 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.50 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" C2' ATP B 801 " pdb=" C1' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" O2' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.61e-01 chirality pdb=" C2' ATP E 801 " pdb=" C1' ATP E 801 " pdb=" C3' ATP E 801 " pdb=" O2' ATP E 801 " both_signs ideal model delta sigma weight residual False -2.68 -2.52 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 2251 not shown) Planarity restraints: 2491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 750 " 0.035 2.00e-02 2.50e+03 6.83e-02 4.67e+01 pdb=" C SER B 750 " -0.118 2.00e-02 2.50e+03 pdb=" O SER B 750 " 0.044 2.00e-02 2.50e+03 pdb=" N GLN B 751 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 750 " -0.034 2.00e-02 2.50e+03 6.74e-02 4.55e+01 pdb=" C SER E 750 " 0.117 2.00e-02 2.50e+03 pdb=" O SER E 750 " -0.044 2.00e-02 2.50e+03 pdb=" N GLN E 751 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 753 " 0.034 2.00e-02 2.50e+03 6.55e-02 4.29e+01 pdb=" C TYR C 753 " -0.113 2.00e-02 2.50e+03 pdb=" O TYR C 753 " 0.042 2.00e-02 2.50e+03 pdb=" N GLY C 754 " 0.038 2.00e-02 2.50e+03 ... (remaining 2488 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 166 2.58 - 3.16: 12235 3.16 - 3.74: 20738 3.74 - 4.32: 28972 4.32 - 4.90: 48751 Nonbonded interactions: 110862 Sorted by model distance: nonbonded pdb=" OG1 THR A 543 " pdb=" O SER A 577 " model vdw 1.998 3.040 nonbonded pdb=" O2B ATP A 801 " pdb="MG MG A 802 " model vdw 2.007 2.170 nonbonded pdb=" O2B ATP C 801 " pdb="MG MG C 802 " model vdw 2.010 2.170 nonbonded pdb=" O3G ATP D 801 " pdb="MG MG D 802 " model vdw 2.016 2.170 nonbonded pdb=" O3BBADP F 802 " pdb="MG MG F 803 " model vdw 2.034 2.170 ... (remaining 110857 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 460 through 706 or (resid 707 through 733 and (name N or n \ ame CA or name C or name O or name CB )) or resid 734 through 751)) selection = (chain 'B' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'C' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'D' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'E' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 706 or (resid 707 through 733 and (name N or name CA or name \ C or name O or name CB )) or resid 734 through 751)) selection = (chain 'F' and (resid 460 through 501 or resid 517 through 577 or (resid 578 and \ (name N or name CA or name C or name O or name CB )) or resid 579 through 612 o \ r resid 620 through 751)) } 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 individual isotropic 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 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: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.078 14266 Z= 0.438 Angle : 1.086 25.212 19345 Z= 0.777 Chirality : 0.046 0.180 2254 Planarity : 0.006 0.068 2491 Dihedral : 9.290 100.257 5362 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -3.52 (0.17), residues: 1777 helix: -1.94 (0.15), residues: 838 sheet: -2.74 (0.33), residues: 187 loop : -2.55 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 640 TYR 0.022 0.002 TYR D 686 PHE 0.019 0.003 PHE A 522 TRP 0.011 0.002 TRP C 749 HIS 0.010 0.002 HIS A 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00832 / 0.44 (14266) covalent geometry : angle 1.08601 / 0.78 (19345) hydrogen bonds : bond 0.15682 / 10.55 ( 571) hydrogen bonds : angle 6.25417 / 4.39 ( 1614) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 471 ASP cc_start: 0.7561 (m-30) cc_final: 0.7322 (m-30) REVERT: D 604 THR cc_start: 0.8873 (m) cc_final: 0.8652 (m) REVERT: E 636 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7248 (pt0) REVERT: E 678 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7652 (ptp-170) REVERT: E 724 GLU cc_start: 0.7464 (tt0) cc_final: 0.6343 (tt0) REVERT: F 517 LYS cc_start: 0.7453 (mtmt) cc_final: 0.7183 (mtpt) REVERT: F 582 ASP cc_start: 0.7193 (m-30) cc_final: 0.6727 (m-30) REVERT: F 681 LYS cc_start: 0.4313 (mtpp) cc_final: 0.3985 (pttt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.1516 time to fit residues: 57.8727 Evaluate side-chains 124 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 546 ASN A 596 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN D 596 HIS D 629 ASN E 575 GLN E 596 HIS F 596 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.145065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110778 restraints weight = 20780.561| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.87 r_work: 0.3279 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (23 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14266 Z= 0.157 Angle : 0.635 9.025 19345 Z= 0.311 Chirality : 0.044 0.153 2254 Planarity : 0.005 0.051 2491 Dihedral : 5.846 78.017 1973 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.01 % Allowed : 7.37 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.68 (0.19), residues: 1777 helix: -0.36 (0.17), residues: 852 sheet: -2.07 (0.35), residues: 185 loop : -1.66 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 677 TYR 0.013 0.001 TYR C 753 PHE 0.021 0.002 PHE C 610 TRP 0.013 0.001 TRP E 749 HIS 0.003 0.001 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (14266) covalent geometry : angle 0.63503 / 0.31 (19345) hydrogen bonds : bond 0.04192 / 2.80 ( 571) hydrogen bonds : angle 4.71547 / 3.31 ( 1614) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 471 ASP cc_start: 0.7951 (m-30) cc_final: 0.7725 (m-30) REVERT: B 616 ASN cc_start: 0.8594 (t0) cc_final: 0.7790 (t0) REVERT: B 618 ASP cc_start: 0.7803 (p0) cc_final: 0.7171 (t70) REVERT: B 719 MET cc_start: 0.7614 (tpp) cc_final: 0.7382 (ttt) REVERT: C 741 GLN cc_start: 0.8560 (mp10) cc_final: 0.8358 (pm20) REVERT: E 636 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7706 (pt0) REVERT: E 678 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7664 (ptp-170) REVERT: E 724 GLU cc_start: 0.7307 (tt0) cc_final: 0.6144 (tt0) REVERT: E 753 TYR cc_start: 0.8458 (m-80) cc_final: 0.8229 (m-80) REVERT: F 470 LEU cc_start: 0.8124 (mt) cc_final: 0.7920 (mt) REVERT: F 529 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5723 (mttp) REVERT: F 681 LYS cc_start: 0.3892 (mtpp) cc_final: 0.3620 (pttt) outliers start: 15 outliers final: 6 residues processed: 181 average time/residue: 0.1339 time to fit residues: 35.2021 Evaluate side-chains 132 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 464 LYS Chi-restraints excluded: chain F residue 529 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 118 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.0020 chunk 108 optimal weight: 0.5980 chunk 130 optimal weight: 0.0000 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107994 restraints weight = 20397.273| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.16 r_work: 0.3230 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14266 Z= 0.113 Angle : 0.558 7.463 19345 Z= 0.270 Chirality : 0.042 0.212 2254 Planarity : 0.005 0.078 2491 Dihedral : 5.272 77.013 1973 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.21 % Allowed : 8.65 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.77 (0.20), residues: 1777 helix: 0.34 (0.18), residues: 867 sheet: -1.57 (0.35), residues: 188 loop : -1.17 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 735 TYR 0.008 0.001 TYR D 647 PHE 0.015 0.001 PHE C 610 TRP 0.011 0.001 TRP E 749 HIS 0.003 0.001 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (14266) covalent geometry : angle 0.55838 / 0.27 (19345) hydrogen bonds : bond 0.03474 / 2.29 ( 571) hydrogen bonds : angle 4.22098 / 2.94 ( 1614) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 ILE cc_start: 0.7825 (mt) cc_final: 0.7517 (pt) REVERT: A 585 ASP cc_start: 0.8027 (t0) cc_final: 0.7671 (t0) REVERT: B 471 ASP cc_start: 0.7929 (m-30) cc_final: 0.7698 (m-30) REVERT: B 616 ASN cc_start: 0.8430 (t0) cc_final: 0.7754 (t0) REVERT: C 475 GLU cc_start: 0.8482 (pm20) cc_final: 0.8117 (mp0) REVERT: C 517 LYS cc_start: 0.7904 (mmmm) cc_final: 0.7461 (tppt) REVERT: C 715 ASP cc_start: 0.8536 (t0) cc_final: 0.8308 (t70) REVERT: C 741 GLN cc_start: 0.8737 (mp10) cc_final: 0.8414 (pm20) REVERT: E 636 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7593 (pt0) REVERT: E 678 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7342 (ptp-170) REVERT: E 719 MET cc_start: 0.7435 (tpp) cc_final: 0.6918 (tpt) REVERT: E 724 GLU cc_start: 0.7139 (tt0) cc_final: 0.5872 (tt0) REVERT: F 574 MET cc_start: 0.7488 (mtt) cc_final: 0.7246 (mtt) REVERT: F 657 GLU cc_start: 0.7471 (tt0) cc_final: 0.7053 (mt-10) REVERT: F 681 LYS cc_start: 0.3613 (mtpp) cc_final: 0.3401 (pttt) outliers start: 18 outliers final: 8 residues processed: 158 average time/residue: 0.1277 time to fit residues: 29.7858 Evaluate side-chains 130 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain F residue 659 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN C 596 HIS ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 GLN ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.099316 restraints weight = 20731.440| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.13 r_work: 0.3099 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14266 Z= 0.177 Angle : 0.596 8.999 19345 Z= 0.288 Chirality : 0.043 0.151 2254 Planarity : 0.004 0.049 2491 Dihedral : 5.274 84.239 1973 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.88 % Allowed : 9.85 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.35 (0.20), residues: 1777 helix: 0.78 (0.18), residues: 856 sheet: -1.25 (0.36), residues: 192 loop : -1.08 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 621 TYR 0.013 0.001 TYR D 647 PHE 0.019 0.002 PHE D 642 TRP 0.013 0.001 TRP E 749 HIS 0.005 0.001 HIS C 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (14266) covalent geometry : angle 0.59608 / 0.29 (19345) hydrogen bonds : bond 0.03801 / 2.46 ( 571) hydrogen bonds : angle 4.17949 / 2.93 ( 1614) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8182 (mt) cc_final: 0.7755 (pt) REVERT: A 585 ASP cc_start: 0.8185 (t0) cc_final: 0.7864 (t0) REVERT: B 471 ASP cc_start: 0.7983 (m-30) cc_final: 0.7748 (m-30) REVERT: B 616 ASN cc_start: 0.8445 (t0) cc_final: 0.7748 (t0) REVERT: C 499 VAL cc_start: 0.8100 (t) cc_final: 0.7772 (m) REVERT: C 517 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7669 (tppt) REVERT: C 636 GLU cc_start: 0.7933 (pm20) cc_final: 0.7668 (pm20) REVERT: C 715 ASP cc_start: 0.8618 (t0) cc_final: 0.8347 (t70) REVERT: C 741 GLN cc_start: 0.8725 (mp10) cc_final: 0.8406 (pm20) REVERT: D 475 GLU cc_start: 0.8654 (pm20) cc_final: 0.8322 (mm-30) REVERT: D 548 SER cc_start: 0.8632 (p) cc_final: 0.8424 (p) REVERT: D 666 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8704 (ttpt) REVERT: E 636 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7838 (pt0) REVERT: E 678 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7493 (ptp-170) REVERT: E 686 TYR cc_start: 0.8651 (m-80) cc_final: 0.8260 (m-80) REVERT: E 719 MET cc_start: 0.7381 (tpp) cc_final: 0.6901 (tpt) REVERT: E 724 GLU cc_start: 0.7253 (tt0) cc_final: 0.6253 (tt0) REVERT: F 520 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6013 (pt) REVERT: F 529 LYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5274 (mttp) REVERT: F 657 GLU cc_start: 0.7507 (tt0) cc_final: 0.7046 (mt-10) REVERT: F 676 LEU cc_start: 0.4178 (OUTLIER) cc_final: 0.3644 (pp) REVERT: F 681 LYS cc_start: 0.3553 (mtpp) cc_final: 0.3316 (pttt) REVERT: G 9 GLU cc_start: 0.8241 (pt0) cc_final: 0.7965 (pt0) outliers start: 28 outliers final: 16 residues processed: 165 average time/residue: 0.1310 time to fit residues: 31.2214 Evaluate side-chains 149 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 529 LYS Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN B 629 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099150 restraints weight = 20827.722| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.11 r_work: 0.3101 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14266 Z= 0.143 Angle : 0.554 6.460 19345 Z= 0.268 Chirality : 0.042 0.146 2254 Planarity : 0.004 0.045 2491 Dihedral : 5.170 79.547 1973 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.94 % Allowed : 10.92 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.11 (0.20), residues: 1777 helix: 0.95 (0.18), residues: 859 sheet: -1.04 (0.38), residues: 182 loop : -0.98 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 630 TYR 0.011 0.001 TYR D 647 PHE 0.016 0.001 PHE A 580 TRP 0.008 0.001 TRP E 749 HIS 0.002 0.000 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (14266) covalent geometry : angle 0.55392 / 0.27 (19345) hydrogen bonds : bond 0.03443 / 2.22 ( 571) hydrogen bonds : angle 4.10003 / 2.86 ( 1614) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8212 (mt) cc_final: 0.7845 (pt) REVERT: A 585 ASP cc_start: 0.8116 (t0) cc_final: 0.7841 (t0) REVERT: B 471 ASP cc_start: 0.7959 (m-30) cc_final: 0.7708 (m-30) REVERT: B 616 ASN cc_start: 0.8517 (t0) cc_final: 0.7716 (t0) REVERT: C 517 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7527 (tppt) REVERT: C 636 GLU cc_start: 0.7955 (pm20) cc_final: 0.7670 (pt0) REVERT: C 715 ASP cc_start: 0.8612 (t0) cc_final: 0.8335 (t70) REVERT: C 741 GLN cc_start: 0.8672 (mp10) cc_final: 0.8291 (pm20) REVERT: D 548 SER cc_start: 0.8587 (p) cc_final: 0.8369 (p) REVERT: D 666 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8778 (ttpt) REVERT: E 636 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7895 (pt0) REVERT: E 686 TYR cc_start: 0.8675 (m-80) cc_final: 0.8331 (m-80) REVERT: E 719 MET cc_start: 0.7276 (tpp) cc_final: 0.6912 (tpt) REVERT: E 724 GLU cc_start: 0.7265 (tt0) cc_final: 0.7061 (tt0) REVERT: E 735 ARG cc_start: 0.7424 (mtp85) cc_final: 0.6892 (mtp85) REVERT: F 657 GLU cc_start: 0.7545 (tt0) cc_final: 0.7117 (mt-10) REVERT: F 676 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.3704 (pp) REVERT: F 681 LYS cc_start: 0.3524 (mtpp) cc_final: 0.3266 (pttt) outliers start: 29 outliers final: 18 residues processed: 159 average time/residue: 0.1235 time to fit residues: 28.9559 Evaluate side-chains 145 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 592 SER Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 62 optimal weight: 0.2980 chunk 132 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099366 restraints weight = 20810.116| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.12 r_work: 0.3105 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14266 Z= 0.122 Angle : 0.536 7.082 19345 Z= 0.258 Chirality : 0.041 0.144 2254 Planarity : 0.004 0.048 2491 Dihedral : 5.032 77.450 1973 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 11.26 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.20), residues: 1777 helix: 1.22 (0.18), residues: 849 sheet: -0.88 (0.38), residues: 182 loop : -0.91 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 621 TYR 0.009 0.001 TYR D 647 PHE 0.015 0.001 PHE A 580 TRP 0.006 0.001 TRP E 749 HIS 0.002 0.000 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14266) covalent geometry : angle 0.53573 / 0.26 (19345) hydrogen bonds : bond 0.03242 / 2.08 ( 571) hydrogen bonds : angle 3.99340 / 2.78 ( 1614) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8264 (mt) cc_final: 0.7895 (pt) REVERT: A 585 ASP cc_start: 0.8225 (t0) cc_final: 0.7971 (t0) REVERT: B 471 ASP cc_start: 0.7923 (m-30) cc_final: 0.7688 (m-30) REVERT: B 616 ASN cc_start: 0.8505 (t0) cc_final: 0.7724 (t0) REVERT: B 747 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8417 (mt-10) REVERT: C 636 GLU cc_start: 0.7961 (pm20) cc_final: 0.7539 (pt0) REVERT: C 741 GLN cc_start: 0.8662 (mp10) cc_final: 0.8276 (pm20) REVERT: D 548 SER cc_start: 0.8541 (p) cc_final: 0.8325 (p) REVERT: D 666 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8736 (ttpt) REVERT: E 471 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: E 636 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7803 (pt0) REVERT: E 686 TYR cc_start: 0.8660 (m-80) cc_final: 0.8310 (m-80) REVERT: E 719 MET cc_start: 0.7389 (tpp) cc_final: 0.7066 (tpt) REVERT: E 735 ARG cc_start: 0.7394 (mtp85) cc_final: 0.6819 (mtp85) REVERT: F 483 THR cc_start: 0.5761 (p) cc_final: 0.5501 (p) REVERT: F 520 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6063 (pt) REVERT: F 657 GLU cc_start: 0.7420 (tt0) cc_final: 0.7037 (mt-10) REVERT: F 676 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.3694 (pp) REVERT: F 681 LYS cc_start: 0.3197 (mtpp) cc_final: 0.2957 (pttt) outliers start: 30 outliers final: 19 residues processed: 148 average time/residue: 0.1172 time to fit residues: 26.1704 Evaluate side-chains 141 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 471 ASP Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 155 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 108 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.2980 chunk 166 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 overall best weight: 0.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100927 restraints weight = 20634.949| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.12 r_work: 0.3126 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14266 Z= 0.099 Angle : 0.525 9.508 19345 Z= 0.249 Chirality : 0.040 0.141 2254 Planarity : 0.004 0.046 2491 Dihedral : 4.904 78.579 1973 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.74 % Allowed : 12.13 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.40 (0.21), residues: 1777 helix: 1.41 (0.19), residues: 853 sheet: -0.75 (0.38), residues: 184 loop : -0.78 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 621 TYR 0.008 0.001 TYR C 753 PHE 0.010 0.001 PHE A 580 TRP 0.007 0.001 TRP D 749 HIS 0.002 0.000 HIS F 573 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (14266) covalent geometry : angle 0.52453 / 0.25 (19345) hydrogen bonds : bond 0.02976 / 1.90 ( 571) hydrogen bonds : angle 3.87730 / 2.70 ( 1614) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8266 (mt) cc_final: 0.7924 (pt) REVERT: A 585 ASP cc_start: 0.8207 (t0) cc_final: 0.7940 (t0) REVERT: A 623 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7668 (m) REVERT: B 471 ASP cc_start: 0.7931 (m-30) cc_final: 0.7691 (m-30) REVERT: B 616 ASN cc_start: 0.8515 (t0) cc_final: 0.7741 (t0) REVERT: B 747 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8413 (mt-10) REVERT: C 636 GLU cc_start: 0.7901 (pm20) cc_final: 0.7534 (pt0) REVERT: C 741 GLN cc_start: 0.8655 (mp10) cc_final: 0.8277 (pm20) REVERT: D 553 THR cc_start: 0.9126 (m) cc_final: 0.8728 (p) REVERT: D 666 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8674 (ttpt) REVERT: E 636 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7794 (pt0) REVERT: E 686 TYR cc_start: 0.8611 (m-80) cc_final: 0.8313 (m-80) REVERT: E 719 MET cc_start: 0.7445 (tpp) cc_final: 0.7090 (tpt) REVERT: E 735 ARG cc_start: 0.7362 (mtp85) cc_final: 0.6776 (mtp85) REVERT: F 520 LEU cc_start: 0.6711 (OUTLIER) cc_final: 0.6090 (pt) REVERT: F 657 GLU cc_start: 0.7374 (tt0) cc_final: 0.7004 (mt-10) REVERT: F 676 LEU cc_start: 0.4412 (OUTLIER) cc_final: 0.3677 (pp) REVERT: F 681 LYS cc_start: 0.3236 (mtpp) cc_final: 0.2995 (pttt) outliers start: 26 outliers final: 19 residues processed: 146 average time/residue: 0.1166 time to fit residues: 26.0113 Evaluate side-chains 144 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 700 LEU Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 125 optimal weight: 0.1980 chunk 116 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 1 optimal weight: 0.0070 chunk 41 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101138 restraints weight = 20695.069| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.10 r_work: 0.3133 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 14266 Z= 0.102 Angle : 0.530 10.131 19345 Z= 0.251 Chirality : 0.040 0.140 2254 Planarity : 0.003 0.048 2491 Dihedral : 4.833 79.367 1973 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.81 % Allowed : 12.06 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.52 (0.21), residues: 1777 helix: 1.51 (0.19), residues: 854 sheet: -0.66 (0.39), residues: 184 loop : -0.72 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 630 TYR 0.015 0.001 TYR B 746 PHE 0.012 0.001 PHE A 580 TRP 0.016 0.001 TRP F 749 HIS 0.001 0.000 HIS A 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (14266) covalent geometry : angle 0.52971 / 0.25 (19345) hydrogen bonds : bond 0.02916 / 1.86 ( 571) hydrogen bonds : angle 3.81561 / 2.66 ( 1614) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8281 (mt) cc_final: 0.7950 (pt) REVERT: A 585 ASP cc_start: 0.8285 (t0) cc_final: 0.8014 (t0) REVERT: B 471 ASP cc_start: 0.7886 (m-30) cc_final: 0.7634 (m-30) REVERT: B 472 GLU cc_start: 0.8032 (tp30) cc_final: 0.7535 (tt0) REVERT: B 616 ASN cc_start: 0.8524 (t0) cc_final: 0.7791 (t0) REVERT: B 747 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8407 (mt-10) REVERT: C 636 GLU cc_start: 0.7829 (pm20) cc_final: 0.7587 (pt0) REVERT: C 741 GLN cc_start: 0.8664 (mp10) cc_final: 0.8285 (pm20) REVERT: D 475 GLU cc_start: 0.8770 (pm20) cc_final: 0.8445 (mm-30) REVERT: D 553 THR cc_start: 0.9114 (m) cc_final: 0.8732 (p) REVERT: E 489 ASP cc_start: 0.8068 (p0) cc_final: 0.7868 (m-30) REVERT: E 636 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7791 (pt0) REVERT: E 686 TYR cc_start: 0.8626 (m-80) cc_final: 0.8311 (m-80) REVERT: E 719 MET cc_start: 0.7427 (tpp) cc_final: 0.7076 (tpt) REVERT: E 727 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7533 (t80) REVERT: E 735 ARG cc_start: 0.7345 (mtp85) cc_final: 0.6762 (mtp85) REVERT: F 520 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6055 (pt) REVERT: F 657 GLU cc_start: 0.7351 (tt0) cc_final: 0.6995 (mt-10) REVERT: F 676 LEU cc_start: 0.4390 (OUTLIER) cc_final: 0.3662 (pp) REVERT: F 681 LYS cc_start: 0.3343 (mtpp) cc_final: 0.3131 (pttt) outliers start: 27 outliers final: 18 residues processed: 149 average time/residue: 0.1093 time to fit residues: 25.1546 Evaluate side-chains 143 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 727 PHE Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 123 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099326 restraints weight = 20921.891| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.18 r_work: 0.3103 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14266 Z= 0.129 Angle : 0.542 8.802 19345 Z= 0.261 Chirality : 0.041 0.143 2254 Planarity : 0.004 0.046 2491 Dihedral : 4.840 78.246 1973 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.68 % Allowed : 12.20 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.54 (0.21), residues: 1777 helix: 1.49 (0.18), residues: 855 sheet: -0.59 (0.39), residues: 184 loop : -0.69 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 630 TYR 0.009 0.001 TYR D 647 PHE 0.009 0.001 PHE E 544 TRP 0.013 0.001 TRP F 749 HIS 0.001 0.000 HIS F 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (14266) covalent geometry : angle 0.54168 / 0.26 (19345) hydrogen bonds : bond 0.03068 / 1.96 ( 571) hydrogen bonds : angle 3.85657 / 2.69 ( 1614) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8286 (mt) cc_final: 0.7942 (pt) REVERT: A 585 ASP cc_start: 0.8328 (t0) cc_final: 0.8054 (t0) REVERT: B 471 ASP cc_start: 0.7915 (m-30) cc_final: 0.7672 (m-30) REVERT: B 609 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 616 ASN cc_start: 0.8528 (t0) cc_final: 0.7796 (t0) REVERT: B 747 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8413 (mt-10) REVERT: C 636 GLU cc_start: 0.7758 (pm20) cc_final: 0.7506 (pt0) REVERT: D 475 GLU cc_start: 0.8707 (pm20) cc_final: 0.8362 (mm-30) REVERT: E 636 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7799 (pt0) REVERT: E 686 TYR cc_start: 0.8653 (m-80) cc_final: 0.8357 (m-80) REVERT: E 719 MET cc_start: 0.7401 (tpp) cc_final: 0.7043 (tpt) REVERT: E 727 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7412 (t80) REVERT: E 735 ARG cc_start: 0.7391 (mtp85) cc_final: 0.6804 (mtp85) REVERT: F 520 LEU cc_start: 0.6735 (OUTLIER) cc_final: 0.6129 (pt) REVERT: F 657 GLU cc_start: 0.7359 (tt0) cc_final: 0.7142 (mt-10) REVERT: F 676 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.3869 (pp) REVERT: F 681 LYS cc_start: 0.3300 (mtpp) cc_final: 0.3026 (pttt) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 0.1097 time to fit residues: 23.8532 Evaluate side-chains 144 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 727 PHE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 2 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.0070 chunk 105 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100080 restraints weight = 20857.730| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.12 r_work: 0.3116 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14266 Z= 0.111 Angle : 0.538 8.790 19345 Z= 0.260 Chirality : 0.040 0.143 2254 Planarity : 0.004 0.046 2491 Dihedral : 4.819 79.108 1973 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.47 % Allowed : 12.73 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.66 (0.21), residues: 1777 helix: 1.59 (0.18), residues: 853 sheet: -0.53 (0.38), residues: 190 loop : -0.63 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 600 TYR 0.008 0.001 TYR C 753 PHE 0.011 0.001 PHE A 580 TRP 0.014 0.001 TRP F 749 HIS 0.001 0.000 HIS E 728 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (14266) covalent geometry : angle 0.53839 / 0.26 (19345) hydrogen bonds : bond 0.03001 / 1.91 ( 571) hydrogen bonds : angle 3.83067 / 2.67 ( 1614) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 473 ILE cc_start: 0.8285 (mt) cc_final: 0.7948 (pt) REVERT: A 585 ASP cc_start: 0.8380 (t0) cc_final: 0.8119 (t0) REVERT: B 471 ASP cc_start: 0.7899 (m-30) cc_final: 0.7653 (m-30) REVERT: B 609 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 616 ASN cc_start: 0.8503 (t0) cc_final: 0.7756 (t0) REVERT: B 747 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8355 (mt-10) REVERT: C 636 GLU cc_start: 0.7814 (pm20) cc_final: 0.7588 (pt0) REVERT: D 475 GLU cc_start: 0.8712 (pm20) cc_final: 0.8293 (tp30) REVERT: E 636 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7769 (pt0) REVERT: E 686 TYR cc_start: 0.8626 (m-80) cc_final: 0.8328 (m-80) REVERT: E 719 MET cc_start: 0.7393 (tpp) cc_final: 0.7041 (tpt) REVERT: E 727 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7374 (t80) REVERT: E 735 ARG cc_start: 0.7325 (mtp85) cc_final: 0.6714 (mtp85) REVERT: F 520 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6107 (pt) REVERT: F 657 GLU cc_start: 0.7421 (tt0) cc_final: 0.7207 (mt-10) REVERT: F 676 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.3871 (pp) REVERT: F 681 LYS cc_start: 0.3361 (mtpp) cc_final: 0.3160 (pttt) outliers start: 22 outliers final: 18 residues processed: 140 average time/residue: 0.1119 time to fit residues: 24.4035 Evaluate side-chains 142 residues out of total 1519 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 577 SER Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 629 ASN Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 744 ASN Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 559 ASP Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 727 PHE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 659 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain G residue 12 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 164 optimal weight: 0.0470 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS B 629 ASN ** C 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099465 restraints weight = 21196.720| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.83 r_work: 0.3110 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14266 Z= 0.154 Angle : 0.558 8.182 19345 Z= 0.271 Chirality : 0.042 0.145 2254 Planarity : 0.004 0.046 2491 Dihedral : 4.869 77.120 1973 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.54 % Allowed : 13.20 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.59 (0.21), residues: 1777 helix: 1.51 (0.18), residues: 853 sheet: -0.55 (0.38), residues: 191 loop : -0.64 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 600 TYR 0.010 0.001 TYR D 647 PHE 0.013 0.001 PHE A 580 TRP 0.014 0.001 TRP F 749 HIS 0.002 0.000 HIS F 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (14266) covalent geometry : angle 0.55810 / 0.27 (19345) hydrogen bonds : bond 0.03286 / 2.11 ( 571) hydrogen bonds : angle 3.91241 / 2.73 ( 1614) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3521.53 seconds wall clock time: 61 minutes 4.29 seconds (3664.29 seconds total)