Starting phenix.real_space_refine on Sat Jul 4 09:38:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.map" model { file = "/net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ola_12975/07_2026/7ola_12975.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 12 5.49 5 Mg 3 5.21 5 S 58 5.16 5 C 12615 2.51 5 N 3282 2.21 5 O 3749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19719 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3664 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3676 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3542 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3042 Classifications: {'peptide': 375} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 360} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2833 Classifications: {'peptide': 349} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2835 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 13, 'TRANS': 334} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.20, per 1000 atoms: 0.21 Number of scatterers: 19719 At special positions: 0 Unit cell: (139.4, 124.64, 126.28, 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 58 16.00 P 12 15.00 Mg 3 11.99 O 3749 8.00 N 3282 7.00 C 12615 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: 1.57 Conformation dependent library (CDL) restraints added in 811.1 milliseconds 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 29 sheets defined 44.3% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 361 Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.506A pdb=" N ILE A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 486 through 502 Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.703A pdb=" N LEU A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 4.025A pdb=" N LYS A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.618A pdb=" N TYR A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 349 through 361 Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 486 through 501 removed outlier: 3.799A pdb=" N MET B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'B' and resid 574 through 582 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.746A pdb=" N LEU B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 646 removed outlier: 4.131A pdb=" N LYS B 644 " --> pdb=" O ASN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 650 through 664 Processing helix chain 'B' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.650A pdb=" N VAL B 710 " --> pdb=" O PRO B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 719 Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.696A pdb=" N GLN B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 339 Processing helix chain 'C' and resid 349 through 361 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 486 through 502 Processing helix chain 'C' and resid 520 through 532 Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 550 through 555 removed outlier: 3.517A pdb=" N GLU C 555 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 582 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 640 through 646 removed outlier: 4.343A pdb=" N LYS C 644 " --> pdb=" O ASN C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 664 Processing helix chain 'C' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 706 through 718 removed outlier: 3.850A pdb=" N VAL C 710 " --> pdb=" O PRO C 706 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR C 714 " --> pdb=" O VAL C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 731 removed outlier: 3.788A pdb=" N PHE C 731 " --> pdb=" O SER C 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 728 through 731' Processing helix chain 'C' and resid 732 through 737 Processing helix chain 'D' and resid 317 through 339 Processing helix chain 'D' and resid 349 through 361 Processing helix chain 'D' and resid 387 through 399 removed outlier: 3.535A pdb=" N ILE D 391 " --> pdb=" O ASN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'D' and resid 486 through 502 Processing helix chain 'D' and resid 520 through 533 Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 640 through 646 removed outlier: 4.036A pdb=" N LYS D 644 " --> pdb=" O ASN D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 Processing helix chain 'D' and resid 672 through 687 Processing helix chain 'E' and resid 317 through 338 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'E' and resid 387 through 399 Processing helix chain 'E' and resid 403 through 418 Processing helix chain 'E' and resid 474 through 483 Processing helix chain 'E' and resid 486 through 501 Processing helix chain 'E' and resid 520 through 532 Processing helix chain 'E' and resid 541 through 545 Processing helix chain 'E' and resid 550 through 555 removed outlier: 3.992A pdb=" N VAL E 553 " --> pdb=" O LYS E 550 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU E 555 " --> pdb=" O SER E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 582 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.587A pdb=" N LEU E 622 " --> pdb=" O THR E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 664 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 326 through 339 Processing helix chain 'F' and resid 349 through 361 Processing helix chain 'F' and resid 387 through 399 removed outlier: 3.515A pdb=" N ILE F 391 " --> pdb=" O ASN F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 418 Processing helix chain 'F' and resid 475 through 483 Processing helix chain 'F' and resid 486 through 502 Processing helix chain 'F' and resid 520 through 532 removed outlier: 3.541A pdb=" N ILE F 532 " --> pdb=" O LEU F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 555 removed outlier: 3.649A pdb=" N VAL F 553 " --> pdb=" O LYS F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 582 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 640 through 646 removed outlier: 3.526A pdb=" N ASP F 646 " --> pdb=" O LYS F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 664 Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 365 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 537 through 539 removed outlier: 6.234A pdb=" N ALA A 538 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP A 563 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 560 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER A 607 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY A 562 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA A 510 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 628 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 512 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 588 Processing sheet with id=AA7, first strand: chain 'B' and resid 363 through 365 Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AA9, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'B' and resid 537 through 539 removed outlier: 6.210A pdb=" N ALA B 538 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP B 563 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 560 " --> pdb=" O ILE B 605 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N SER B 607 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY B 562 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA B 510 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 628 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 512 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 571 Processing sheet with id=AB3, first strand: chain 'B' and resid 585 through 588 Processing sheet with id=AB4, first strand: chain 'C' and resid 363 through 365 Processing sheet with id=AB5, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AB6, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AB7, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.254A pdb=" N ALA C 538 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA C 510 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 628 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE C 512 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 588 Processing sheet with id=AB9, first strand: chain 'D' and resid 363 through 365 Processing sheet with id=AC1, first strand: chain 'D' and resid 429 through 432 Processing sheet with id=AC2, first strand: chain 'D' and resid 469 through 470 Processing sheet with id=AC3, first strand: chain 'D' and resid 537 through 539 removed outlier: 3.982A pdb=" N ASP D 564 " --> pdb=" O SER D 607 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE D 511 " --> pdb=" O GLN D 606 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR D 608 " --> pdb=" O ILE D 511 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE D 513 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ALA D 510 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 628 " --> pdb=" O ALA D 510 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE D 512 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 363 through 365 Processing sheet with id=AC5, first strand: chain 'E' and resid 429 through 431 Processing sheet with id=AC6, first strand: chain 'E' and resid 537 through 538 removed outlier: 6.252A pdb=" N VAL E 560 " --> pdb=" O ILE E 605 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER E 607 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY E 562 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA E 510 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL E 628 " --> pdb=" O ALA E 510 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE E 512 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 586 through 590 removed outlier: 4.703A pdb=" N PHE E 590 " --> pdb=" O PRO E 594 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 363 through 365 Processing sheet with id=AC9, first strand: chain 'F' and resid 429 through 432 Processing sheet with id=AD1, first strand: chain 'F' and resid 537 through 538 removed outlier: 5.966A pdb=" N ALA F 538 " --> pdb=" O ILE F 561 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA F 510 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL F 628 " --> pdb=" O ALA F 510 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE F 512 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 586 through 588 795 hydrogen bonds defined for protein. 2262 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: 3.31 Time building geometry restraints manager: 2.12 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: 6307 1.34 - 1.46: 3442 1.46 - 1.58: 10262 1.58 - 1.69: 20 1.69 - 1.81: 95 Bond restraints: 20126 Sorted by residual: bond pdb=" N3B ANP A1201 " pdb=" PG ANP A1201 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N3B ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N3B ANP D1201 " pdb=" PG ANP D1201 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" N3B ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" O3A ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 20121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 26734 1.93 - 3.86: 393 3.86 - 5.78: 55 5.78 - 7.71: 16 7.71 - 9.64: 7 Bond angle restraints: 27205 Sorted by residual: angle pdb=" C LEU B 739 " pdb=" CA LEU B 739 " pdb=" CB LEU B 739 " ideal model delta sigma weight residual 117.23 110.55 6.68 1.36e+00 5.41e-01 2.41e+01 angle pdb=" N ILE B 760 " pdb=" CA ILE B 760 " pdb=" C ILE B 760 " ideal model delta sigma weight residual 113.71 109.90 3.81 9.50e-01 1.11e+00 1.61e+01 angle pdb=" CA LEU B 739 " pdb=" C LEU B 739 " pdb=" N GLU B 740 " ideal model delta sigma weight residual 119.98 116.93 3.05 8.50e-01 1.38e+00 1.28e+01 angle pdb=" CA GLU D 547 " pdb=" C GLU D 547 " pdb=" O GLU D 547 " ideal model delta sigma weight residual 121.38 117.59 3.79 1.06e+00 8.90e-01 1.28e+01 angle pdb=" C VAL B 705 " pdb=" CA VAL B 705 " pdb=" CB VAL B 705 " ideal model delta sigma weight residual 114.35 110.67 3.68 1.06e+00 8.90e-01 1.20e+01 ... (remaining 27200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 11854 35.34 - 70.69: 177 70.69 - 106.03: 45 106.03 - 141.38: 1 141.38 - 176.72: 3 Dihedral angle restraints: 12080 sinusoidal: 5049 harmonic: 7031 Sorted by residual: dihedral pdb=" O1A ANP B1201 " pdb=" O3A ANP B1201 " pdb=" PA ANP B1201 " pdb=" PB ANP B1201 " ideal model delta sinusoidal sigma weight residual 83.11 -93.61 176.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP D1201 " pdb=" O3A ANP D1201 " pdb=" PA ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sinusoidal sigma weight residual 83.11 -77.29 160.40 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A1201 " pdb=" O3A ANP A1201 " pdb=" PA ANP A1201 " pdb=" PB ANP A1201 " ideal model delta sinusoidal sigma weight residual 83.11 -68.37 151.48 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 12077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2682 0.073 - 0.146: 272 0.146 - 0.219: 8 0.219 - 0.292: 3 0.292 - 0.365: 3 Chirality restraints: 2968 Sorted by residual: chirality pdb=" C3' ANP C1201 " pdb=" C2' ANP C1201 " pdb=" C4' ANP C1201 " pdb=" O3' ANP C1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3' ANP A1201 " pdb=" C2' ANP A1201 " pdb=" C4' ANP A1201 " pdb=" O3' ANP A1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C3' ANP D1201 " pdb=" C2' ANP D1201 " pdb=" C4' ANP D1201 " pdb=" O3' ANP D1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2965 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 611 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO E 612 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 612 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 612 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 322 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" CD GLN A 322 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN A 322 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN A 322 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP B1201 " 0.016 2.00e-02 2.50e+03 7.97e-03 1.75e+00 pdb=" C2 ANP B1201 " -0.001 2.00e-02 2.50e+03 pdb=" C4 ANP B1201 " -0.004 2.00e-02 2.50e+03 pdb=" C5 ANP B1201 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ANP B1201 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ANP B1201 " 0.006 2.00e-02 2.50e+03 pdb=" N1 ANP B1201 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ANP B1201 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ANP B1201 " 0.009 2.00e-02 2.50e+03 pdb=" N7 ANP B1201 " -0.007 2.00e-02 2.50e+03 pdb=" N9 ANP B1201 " -0.015 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 172 2.60 - 3.17: 17275 3.17 - 3.75: 31111 3.75 - 4.32: 43537 4.32 - 4.90: 69984 Nonbonded interactions: 162079 Sorted by model distance: nonbonded pdb=" O2B ANP B1201 " pdb="MG MG B1202 " model vdw 2.023 2.170 nonbonded pdb=" O1B ANP D1201 " pdb="MG MG D1202 " model vdw 2.090 2.170 nonbonded pdb=" NH1 ARG F 328 " pdb=" OE1 GLU F 399 " model vdw 2.205 3.120 nonbonded pdb=" OG SER C 579 " pdb=" OD2 ASP D 563 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP C 563 " pdb=" N ASP C 564 " model vdw 2.237 3.120 ... (remaining 162074 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 316 through 697 or resid 703 through 736 or (resid 737 and \ (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or n \ ame CE1 or name NE2)) or resid 741 through 742 or (resid 743 and (name N or name \ CA or name C or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 745 through 747 o \ r (resid 748 and (name N or name CA or name C or name CB or name CG or name CD o \ r name OE1 or name NE2)) or resid 749 or resid 759 through 762 or resid 766 thro \ ugh 1201)) selection = (chain 'B' and (resid 316 through 697 or resid 703 through 736 or (resid 737 and \ (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or n \ ame CE1 or name NE2)) or resid 741 through 742 or (resid 743 and (name N or name \ CA or name C or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 745 through 750 o \ r resid 759 through 762 or resid 766 through 1201)) selection = (chain 'C' and (resid 316 through 747 or (resid 748 and (name N or name CA or na \ me C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 749 or \ resid 759 through 1201)) } ncs_group { reference = (chain 'D' and (resid 316 through 514 or (resid 515 and (name N or name CA or na \ me C )) or resid 519 through 563 or resid 565 or (resid 566 and (name N or name \ CA or name C or name CB or name CG or name CD )) or resid 574 or resid 576 throu \ gh 633 or (resid 634 and (name N or name CA or name C or name CB or name CG or n \ ame CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 635 and (nam \ e N or name CA or name C or name CB or name CG or name OD1 or name ND2)) or resi \ d 641 through 671 or (resid 672 and (name N or name CA or name C or name CB or n \ ame CG or name CD )))) selection = (chain 'E' and (resid 316 through 544 or (resid 545 and (name N or name CA or na \ me C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ )) or resid 546 through 565 or (resid 566 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 575 through 585 or resid 587 throu \ gh 588 or (resid 589 and (name N or name CA or name C or name CB or name CG or n \ ame CD or name OE1 or name OE2)) or resid 590 through 591 or (resid 592 and (nam \ e N or name CA or name C or name O or name CB )) or resid 593 through 634 or (re \ sid 640 and (name N or name CA or name C or name CB or name CG or name OD1 or na \ me ND2)) or resid 641 through 671 or (resid 672 and (name N or name CA or name C \ or name CB or name CG or name CD )))) selection = (chain 'F' and (resid 316 through 514 or (resid 515 and (name N or name CA or na \ me C )) or resid 519 through 544 or (resid 545 and (name N or name CA or name C \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or resid 546 through 563 or resid 565 through 574 or resid 576 through 585 o \ r resid 587 through 588 or (resid 589 and (name N or name CA or name C or name C \ B or name CG or name CD or name OE1 or name OE2)) or resid 590 through 591 or (r \ esid 592 and (name N or name CA or name C or name O or name CB )) or resid 593 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 635 or re \ sid 641 through 672)) } 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=1.00 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: 3.130 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: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.320 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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 : 0.004 0.161 20126 Z= 0.218 Angle : 0.585 9.638 27205 Z= 0.324 Chirality : 0.044 0.365 2968 Planarity : 0.003 0.039 3480 Dihedral : 15.066 176.723 7538 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 1.22 (0.18), residues: 2347 helix: 2.12 (0.17), residues: 987 sheet: -0.33 (0.30), residues: 287 loop : -0.05 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 597 TYR 0.020 0.001 TYR B 717 PHE 0.017 0.001 PHE A 713 TRP 0.009 0.001 TRP E 478 HIS 0.004 0.001 HIS F 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.22 (20126) covalent geometry : angle 0.58501 / 0.32 (27205) hydrogen bonds : bond 0.13797 / 9.55 ( 795) hydrogen bonds : angle 5.14571 / 3.81 ( 2262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.723 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7929 (t80) cc_final: 0.7258 (t80) REVERT: A 743 TRP cc_start: 0.4233 (t-100) cc_final: 0.3460 (t-100) REVERT: B 709 ILE cc_start: 0.9172 (pt) cc_final: 0.8832 (pt) REVERT: C 692 PHE cc_start: 0.8205 (t80) cc_final: 0.7923 (t80) REVERT: E 611 MET cc_start: 0.7897 (mmm) cc_final: 0.7070 (ttm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1197 time to fit residues: 18.6237 Evaluate side-chains 74 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 766 ASN B 609 ASN C 358 ASN C 519 ASN ** C 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 576 ASN F 358 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.073533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051488 restraints weight = 71360.143| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.73 r_work: 0.2746 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20126 Z= 0.117 Angle : 0.469 5.363 27205 Z= 0.257 Chirality : 0.042 0.169 2968 Planarity : 0.003 0.033 3480 Dihedral : 7.841 176.280 2588 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.32 % Allowed : 3.79 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2347 helix: 2.13 (0.17), residues: 990 sheet: -0.59 (0.30), residues: 283 loop : 0.04 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 328 TYR 0.028 0.001 TYR A 717 PHE 0.011 0.001 PHE C 697 TRP 0.007 0.001 TRP A 478 HIS 0.005 0.001 HIS F 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (20126) covalent geometry : angle 0.46894 / 0.26 (27205) hydrogen bonds : bond 0.03847 / 2.54 ( 795) hydrogen bonds : angle 4.41576 / 3.25 ( 2262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.670 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 499 ASP cc_start: 0.9272 (t70) cc_final: 0.9004 (t0) REVERT: A 732 TYR cc_start: 0.7985 (t80) cc_final: 0.7240 (t80) REVERT: A 743 TRP cc_start: 0.4225 (t-100) cc_final: 0.3483 (t-100) REVERT: C 563 ASP cc_start: 0.8223 (p0) cc_final: 0.7535 (t0) REVERT: C 717 TYR cc_start: 0.7194 (p90) cc_final: 0.6979 (p90) REVERT: E 331 MET cc_start: 0.9048 (mtp) cc_final: 0.8587 (mtp) REVERT: E 611 MET cc_start: 0.8506 (mmm) cc_final: 0.8021 (tpp) outliers start: 7 outliers final: 5 residues processed: 84 average time/residue: 0.1230 time to fit residues: 17.1567 Evaluate side-chains 81 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain F residue 484 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 94 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 525 GLN C 358 ASN ** C 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.073472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.051551 restraints weight = 71651.888| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 3.69 r_work: 0.2755 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20126 Z= 0.102 Angle : 0.441 5.207 27205 Z= 0.241 Chirality : 0.041 0.179 2968 Planarity : 0.003 0.031 3480 Dihedral : 7.619 176.094 2588 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.46 % Allowed : 5.02 % Favored : 94.53 % 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: 1.17 (0.18), residues: 2347 helix: 2.10 (0.17), residues: 1002 sheet: -0.62 (0.31), residues: 275 loop : -0.05 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 759 TYR 0.023 0.001 TYR A 717 PHE 0.030 0.001 PHE A 713 TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (20126) covalent geometry : angle 0.44072 / 0.24 (27205) hydrogen bonds : bond 0.03349 / 2.22 ( 795) hydrogen bonds : angle 4.20523 / 3.10 ( 2262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.721 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 499 ASP cc_start: 0.9297 (t70) cc_final: 0.9059 (t0) REVERT: A 732 TYR cc_start: 0.7931 (t80) cc_final: 0.7189 (t80) REVERT: A 743 TRP cc_start: 0.4179 (t-100) cc_final: 0.3408 (t-100) REVERT: B 564 ASP cc_start: 0.9078 (t0) cc_final: 0.8762 (t70) REVERT: C 563 ASP cc_start: 0.8232 (p0) cc_final: 0.7969 (p0) REVERT: C 717 TYR cc_start: 0.7182 (p90) cc_final: 0.6936 (p90) REVERT: E 331 MET cc_start: 0.9064 (mtp) cc_final: 0.8680 (mtp) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.1306 time to fit residues: 19.2227 Evaluate side-chains 83 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 207 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 686 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 525 GLN F 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050374 restraints weight = 72203.544| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.68 r_work: 0.2718 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20126 Z= 0.146 Angle : 0.460 7.500 27205 Z= 0.249 Chirality : 0.042 0.176 2968 Planarity : 0.003 0.037 3480 Dihedral : 7.564 176.581 2588 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.68 % Allowed : 6.34 % Favored : 92.97 % 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: 1.19 (0.18), residues: 2347 helix: 2.14 (0.17), residues: 998 sheet: -0.77 (0.30), residues: 285 loop : -0.00 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 759 TYR 0.011 0.001 TYR A 717 PHE 0.035 0.001 PHE A 713 TRP 0.007 0.001 TRP A 478 HIS 0.005 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (20126) covalent geometry : angle 0.46021 / 0.25 (27205) hydrogen bonds : bond 0.03384 / 2.22 ( 795) hydrogen bonds : angle 4.25038 / 3.14 ( 2262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.814 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 732 TYR cc_start: 0.7978 (t80) cc_final: 0.7233 (t80) REVERT: A 743 TRP cc_start: 0.4108 (t-100) cc_final: 0.3294 (t-100) REVERT: B 564 ASP cc_start: 0.9211 (t0) cc_final: 0.9007 (t0) REVERT: B 697 PHE cc_start: 0.7709 (m-10) cc_final: 0.7392 (m-80) REVERT: B 759 ARG cc_start: 0.7366 (mpp-170) cc_final: 0.6925 (mpp-170) REVERT: C 563 ASP cc_start: 0.8347 (p0) cc_final: 0.8113 (p0) REVERT: C 609 ASN cc_start: 0.9366 (OUTLIER) cc_final: 0.8962 (m-40) REVERT: C 717 TYR cc_start: 0.7167 (p90) cc_final: 0.6925 (p90) REVERT: D 499 ASP cc_start: 0.9233 (t0) cc_final: 0.8898 (m-30) REVERT: E 331 MET cc_start: 0.9093 (mtp) cc_final: 0.8688 (mtp) outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 0.1259 time to fit residues: 19.3473 Evaluate side-chains 82 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 195 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.050992 restraints weight = 71835.117| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.70 r_work: 0.2739 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20126 Z= 0.104 Angle : 0.437 7.262 27205 Z= 0.238 Chirality : 0.041 0.143 2968 Planarity : 0.003 0.038 3480 Dihedral : 7.510 175.175 2588 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.78 % Allowed : 6.98 % Favored : 92.24 % 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: 1.17 (0.18), residues: 2347 helix: 2.14 (0.17), residues: 998 sheet: -0.85 (0.31), residues: 266 loop : -0.02 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.012 0.001 TYR A 708 PHE 0.037 0.001 PHE A 713 TRP 0.006 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (20126) covalent geometry : angle 0.43744 / 0.24 (27205) hydrogen bonds : bond 0.03157 / 2.08 ( 795) hydrogen bonds : angle 4.14421 / 3.06 ( 2262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.816 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 732 TYR cc_start: 0.7963 (t80) cc_final: 0.7211 (t80) REVERT: A 743 TRP cc_start: 0.4112 (t-100) cc_final: 0.3275 (t-100) REVERT: B 564 ASP cc_start: 0.9220 (t0) cc_final: 0.8977 (t0) REVERT: B 697 PHE cc_start: 0.7637 (m-10) cc_final: 0.7335 (m-80) REVERT: B 759 ARG cc_start: 0.7377 (mpp-170) cc_final: 0.7160 (mpp-170) REVERT: C 563 ASP cc_start: 0.8351 (p0) cc_final: 0.8136 (p0) REVERT: C 717 TYR cc_start: 0.7242 (p90) cc_final: 0.7009 (p90) REVERT: D 499 ASP cc_start: 0.9234 (t0) cc_final: 0.8888 (m-30) REVERT: E 331 MET cc_start: 0.9067 (mtp) cc_final: 0.8587 (mtp) REVERT: E 582 THR cc_start: 0.9018 (OUTLIER) cc_final: 0.8801 (p) outliers start: 17 outliers final: 10 residues processed: 89 average time/residue: 0.1246 time to fit residues: 18.5223 Evaluate side-chains 84 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 187 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.0670 chunk 29 optimal weight: 8.9990 chunk 156 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.073656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051705 restraints weight = 71497.508| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.71 r_work: 0.2769 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20126 Z= 0.089 Angle : 0.431 8.546 27205 Z= 0.234 Chirality : 0.041 0.189 2968 Planarity : 0.003 0.039 3480 Dihedral : 7.425 173.929 2588 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.50 % Allowed : 7.89 % Favored : 91.61 % 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: 1.23 (0.18), residues: 2347 helix: 2.18 (0.17), residues: 997 sheet: -0.67 (0.32), residues: 254 loop : -0.03 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 759 TYR 0.012 0.001 TYR A 708 PHE 0.026 0.001 PHE B 735 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS F 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 (20126) covalent geometry : angle 0.43122 / 0.23 (27205) hydrogen bonds : bond 0.02898 / 1.91 ( 795) hydrogen bonds : angle 4.02732 / 2.98 ( 2262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.890 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 611 MET cc_start: 0.8395 (mmm) cc_final: 0.7914 (tmm) REVERT: A 732 TYR cc_start: 0.7920 (t80) cc_final: 0.7187 (t80) REVERT: A 743 TRP cc_start: 0.4113 (t-100) cc_final: 0.3251 (t-100) REVERT: B 564 ASP cc_start: 0.9209 (t0) cc_final: 0.8912 (t0) REVERT: B 697 PHE cc_start: 0.7730 (m-10) cc_final: 0.7422 (m-80) REVERT: C 563 ASP cc_start: 0.8345 (p0) cc_final: 0.8105 (p0) REVERT: C 717 TYR cc_start: 0.7220 (p90) cc_final: 0.6994 (p90) REVERT: D 499 ASP cc_start: 0.9225 (t0) cc_final: 0.8917 (m-30) REVERT: E 331 MET cc_start: 0.9093 (mtp) cc_final: 0.8660 (mtp) REVERT: E 582 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8824 (p) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.1261 time to fit residues: 18.1527 Evaluate side-chains 82 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 34 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 191 optimal weight: 0.0470 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 216 optimal weight: 9.9990 chunk 222 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051355 restraints weight = 72185.441| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.73 r_work: 0.2751 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20126 Z= 0.101 Angle : 0.436 8.823 27205 Z= 0.236 Chirality : 0.041 0.162 2968 Planarity : 0.003 0.041 3480 Dihedral : 7.400 174.710 2588 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.59 % Allowed : 8.39 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.26 (0.18), residues: 2347 helix: 2.20 (0.17), residues: 997 sheet: -0.75 (0.33), residues: 233 loop : -0.00 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 759 TYR 0.012 0.001 TYR B 717 PHE 0.056 0.001 PHE A 713 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS F 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (20126) covalent geometry : angle 0.43578 / 0.24 (27205) hydrogen bonds : bond 0.02943 / 1.93 ( 795) hydrogen bonds : angle 4.01734 / 2.97 ( 2262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.719 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 611 MET cc_start: 0.8357 (mmm) cc_final: 0.7892 (tmm) REVERT: A 732 TYR cc_start: 0.7896 (t80) cc_final: 0.7174 (t80) REVERT: A 743 TRP cc_start: 0.4177 (t-100) cc_final: 0.3300 (t-100) REVERT: B 563 ASP cc_start: 0.8326 (p0) cc_final: 0.8031 (p0) REVERT: B 564 ASP cc_start: 0.9253 (t0) cc_final: 0.8857 (t0) REVERT: B 697 PHE cc_start: 0.7772 (m-10) cc_final: 0.7468 (m-80) REVERT: C 563 ASP cc_start: 0.8371 (p0) cc_final: 0.8146 (p0) REVERT: C 717 TYR cc_start: 0.7295 (p90) cc_final: 0.7076 (p90) REVERT: D 499 ASP cc_start: 0.9261 (t0) cc_final: 0.8961 (m-30) REVERT: D 658 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9373 (tp) REVERT: E 331 MET cc_start: 0.9071 (mtp) cc_final: 0.8612 (mtp) REVERT: E 477 ARG cc_start: 0.9162 (mmp80) cc_final: 0.8922 (mmp80) REVERT: E 582 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8820 (p) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.1296 time to fit residues: 18.5355 Evaluate side-chains 85 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 139 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** 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 = 0.3516 r_free = 0.3516 target = 0.073228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051256 restraints weight = 71565.478| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.70 r_work: 0.2747 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20126 Z= 0.106 Angle : 0.435 10.858 27205 Z= 0.237 Chirality : 0.041 0.164 2968 Planarity : 0.003 0.039 3480 Dihedral : 7.400 175.609 2588 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.68 % Allowed : 8.62 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.18), residues: 2347 helix: 2.19 (0.17), residues: 997 sheet: -0.86 (0.32), residues: 248 loop : -0.02 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.012 0.001 TYR A 708 PHE 0.031 0.001 PHE B 735 TRP 0.005 0.001 TRP A 478 HIS 0.004 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (20126) covalent geometry : angle 0.43504 / 0.24 (27205) hydrogen bonds : bond 0.02970 / 1.95 ( 795) hydrogen bonds : angle 4.01618 / 2.96 ( 2262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.822 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 611 MET cc_start: 0.8347 (mmm) cc_final: 0.7887 (tmm) REVERT: A 732 TYR cc_start: 0.7877 (t80) cc_final: 0.7160 (t80) REVERT: A 743 TRP cc_start: 0.4168 (t-100) cc_final: 0.3277 (t-100) REVERT: B 563 ASP cc_start: 0.8346 (p0) cc_final: 0.8046 (p0) REVERT: B 564 ASP cc_start: 0.9279 (t0) cc_final: 0.8859 (t0) REVERT: B 664 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9335 (pt) REVERT: B 697 PHE cc_start: 0.7746 (m-10) cc_final: 0.7441 (m-80) REVERT: C 563 ASP cc_start: 0.8364 (p0) cc_final: 0.8159 (p0) REVERT: D 499 ASP cc_start: 0.9271 (t0) cc_final: 0.8974 (m-30) REVERT: D 658 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9372 (tp) REVERT: E 331 MET cc_start: 0.9082 (mtp) cc_final: 0.8579 (mtp) REVERT: E 582 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8812 (p) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.1347 time to fit residues: 20.1612 Evaluate side-chains 87 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 186 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 0.2980 chunk 213 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 205 optimal weight: 0.2980 chunk 196 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051105 restraints weight = 71640.493| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.71 r_work: 0.2744 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20126 Z= 0.110 Angle : 0.452 10.534 27205 Z= 0.244 Chirality : 0.041 0.159 2968 Planarity : 0.003 0.039 3480 Dihedral : 7.423 176.233 2588 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.55 % Allowed : 9.03 % Favored : 90.42 % 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: 1.20 (0.18), residues: 2347 helix: 2.17 (0.17), residues: 997 sheet: -0.80 (0.32), residues: 262 loop : -0.03 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.016 0.001 TYR B 717 PHE 0.073 0.001 PHE A 713 TRP 0.005 0.001 TRP A 478 HIS 0.004 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (20126) covalent geometry : angle 0.45192 / 0.24 (27205) hydrogen bonds : bond 0.02999 / 1.97 ( 795) hydrogen bonds : angle 4.01486 / 2.96 ( 2262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.717 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 611 MET cc_start: 0.8410 (mmm) cc_final: 0.7878 (tmm) REVERT: A 732 TYR cc_start: 0.7884 (t80) cc_final: 0.7172 (t80) REVERT: A 743 TRP cc_start: 0.4213 (t-100) cc_final: 0.3298 (t-100) REVERT: B 563 ASP cc_start: 0.8320 (p0) cc_final: 0.8036 (p0) REVERT: B 564 ASP cc_start: 0.9279 (t0) cc_final: 0.8860 (t0) REVERT: B 664 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9332 (pt) REVERT: B 697 PHE cc_start: 0.7798 (m-10) cc_final: 0.7504 (m-80) REVERT: C 563 ASP cc_start: 0.8370 (p0) cc_final: 0.8152 (p0) REVERT: D 499 ASP cc_start: 0.9271 (t0) cc_final: 0.8979 (m-30) REVERT: D 658 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9379 (tp) REVERT: E 331 MET cc_start: 0.9092 (mtp) cc_final: 0.8590 (mtp) REVERT: E 501 MET cc_start: 0.9064 (mtm) cc_final: 0.8762 (pmm) REVERT: E 582 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8808 (p) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.1302 time to fit residues: 18.9766 Evaluate side-chains 86 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 180 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 721 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 609 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.048995 restraints weight = 72435.142| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.64 r_work: 0.2681 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20126 Z= 0.214 Angle : 0.521 13.381 27205 Z= 0.279 Chirality : 0.043 0.157 2968 Planarity : 0.003 0.038 3480 Dihedral : 7.603 178.339 2588 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.68 % Allowed : 9.17 % Favored : 90.15 % 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: 1.10 (0.18), residues: 2347 helix: 2.07 (0.17), residues: 998 sheet: -0.81 (0.30), residues: 289 loop : -0.03 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.014 0.001 TYR A 708 PHE 0.033 0.001 PHE B 735 TRP 0.008 0.001 TRP B 473 HIS 0.006 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (20126) covalent geometry : angle 0.52068 / 0.28 (27205) hydrogen bonds : bond 0.03690 / 2.41 ( 795) hydrogen bonds : angle 4.33502 / 3.18 ( 2262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.749 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 611 MET cc_start: 0.8403 (mmm) cc_final: 0.7949 (tmm) REVERT: A 732 TYR cc_start: 0.7923 (t80) cc_final: 0.7191 (t80) REVERT: A 743 TRP cc_start: 0.4188 (t-100) cc_final: 0.3275 (t-100) REVERT: B 563 ASP cc_start: 0.8406 (p0) cc_final: 0.8115 (p0) REVERT: B 564 ASP cc_start: 0.9338 (t0) cc_final: 0.8923 (t0) REVERT: B 697 PHE cc_start: 0.7813 (m-10) cc_final: 0.7550 (m-80) REVERT: C 563 ASP cc_start: 0.8428 (p0) cc_final: 0.8226 (p0) REVERT: C 609 ASN cc_start: 0.9414 (OUTLIER) cc_final: 0.9042 (m110) REVERT: D 499 ASP cc_start: 0.9254 (t0) cc_final: 0.8966 (m-30) REVERT: D 658 LEU cc_start: 0.9766 (OUTLIER) cc_final: 0.9415 (tp) REVERT: E 331 MET cc_start: 0.9116 (mtp) cc_final: 0.8598 (mtp) REVERT: E 501 MET cc_start: 0.9003 (mtm) cc_final: 0.8741 (pmm) REVERT: E 582 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8783 (p) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 0.1278 time to fit residues: 17.8460 Evaluate side-chains 83 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 609 ASN Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 484 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 150 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.071325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049143 restraints weight = 72380.515| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.64 r_work: 0.2683 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20126 Z= 0.184 Angle : 0.694 59.199 27205 Z= 0.402 Chirality : 0.042 0.257 2968 Planarity : 0.003 0.040 3480 Dihedral : 7.645 178.383 2588 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.89 % Rotamer: Outliers : 0.55 % Allowed : 9.35 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.11 (0.18), residues: 2347 helix: 2.08 (0.17), residues: 998 sheet: -0.81 (0.30), residues: 288 loop : -0.05 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 759 TYR 0.015 0.001 TYR B 708 PHE 0.032 0.001 PHE A 713 TRP 0.007 0.001 TRP A 478 HIS 0.006 0.001 HIS B 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20126) covalent geometry : angle 0.69352 / 0.40 (27205) hydrogen bonds : bond 0.03655 / 2.38 ( 795) hydrogen bonds : angle 4.33262 / 3.18 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4004.02 seconds wall clock time: 69 minutes 40.60 seconds (4180.60 seconds total)