Starting phenix.real_space_refine on Thu Mar 5 06:24:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ola_12975/03_2026/7ola_12975.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ola_12975/03_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_12975/03_2026/7ola_12975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ola_12975/03_2026/7ola_12975.map" model { file = "/net/cci-nas-00/data/ceres_data/7ola_12975/03_2026/7ola_12975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ola_12975/03_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-5986/lib/python3.9/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: 4.66, per 1000 atoms: 0.24 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: 1.54 Conformation dependent library (CDL) restraints added in 863.3 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: 0.82 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: 3.46 Time building geometry restraints manager: 2.14 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: 11882 35.34 - 70.69: 232 70.69 - 106.03: 74 106.03 - 141.38: 1 141.38 - 176.72: 3 Dihedral angle restraints: 12192 sinusoidal: 5161 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 12189 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: 3.260 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.510 Find NCS groups from input model: 0.420 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: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 16.471 176.723 7650 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 covalent geometry : bond 0.00401 (20126) covalent geometry : angle 0.58501 (27205) hydrogen bonds : bond 0.13797 ( 795) hydrogen bonds : angle 5.14571 ( 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 : 0.828 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: 0.1299 time to fit residues: 20.1305 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 : 0.740 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.073535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051492 restraints weight = 71390.030| |-----------------------------------------------------------------------------| 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: 0.8744 moved from start: 0.0754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20126 Z= 0.118 Angle : 0.480 5.520 27205 Z= 0.259 Chirality : 0.042 0.158 2968 Planarity : 0.003 0.033 3480 Dihedral : 11.100 173.743 2700 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.32 % Allowed : 3.88 % Favored : 95.80 % 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 : 0.05 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 328 TYR 0.029 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 covalent geometry : bond 0.00254 (20126) covalent geometry : angle 0.48029 (27205) hydrogen bonds : bond 0.03813 ( 795) hydrogen bonds : angle 4.40829 ( 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 91 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.876 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: 0.9271 (t70) cc_final: 0.9004 (t0) REVERT: A 732 TYR cc_start: 0.7985 (t80) cc_final: 0.7242 (t80) REVERT: A 743 TRP cc_start: 0.4281 (t-100) cc_final: 0.3525 (t-100) REVERT: C 563 ASP cc_start: 0.8228 (p0) cc_final: 0.7537 (t0) REVERT: C 717 TYR cc_start: 0.7194 (p90) cc_final: 0.6958 (p90) REVERT: E 331 MET cc_start: 0.9051 (mtp) cc_final: 0.8588 (mtp) REVERT: E 611 MET cc_start: 0.8507 (mmm) cc_final: 0.8025 (tpp) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.1336 time to fit residues: 19.1785 Evaluate side-chains 82 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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: 0.9980 chunk 135 optimal weight: 0.7980 chunk 13 optimal weight: 0.0270 chunk 88 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3532 r_free = 0.3532 target = 0.073933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052002 restraints weight = 71860.921| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.72 r_work: 0.2772 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20126 Z= 0.093 Angle : 0.445 5.541 27205 Z= 0.241 Chirality : 0.041 0.173 2968 Planarity : 0.003 0.031 3480 Dihedral : 9.353 166.262 2700 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.41 % Allowed : 5.16 % Favored : 94.43 % 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: 2.09 (0.17), residues: 1004 sheet: -0.60 (0.32), residues: 248 loop : -0.03 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 759 TYR 0.021 0.001 TYR A 717 PHE 0.028 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 covalent geometry : bond 0.00194 (20126) covalent geometry : angle 0.44528 (27205) hydrogen bonds : bond 0.03264 ( 795) hydrogen bonds : angle 4.17427 ( 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: 9 poor density : 84 time to evaluate : 0.807 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: 0.9278 (t70) cc_final: 0.9014 (t0) REVERT: A 732 TYR cc_start: 0.7928 (t80) cc_final: 0.7195 (t80) REVERT: A 743 TRP cc_start: 0.4164 (t-100) cc_final: 0.3398 (t-100) REVERT: B 564 ASP cc_start: 0.9071 (t0) cc_final: 0.8737 (t70) REVERT: C 563 ASP cc_start: 0.8227 (p0) cc_final: 0.7954 (p0) REVERT: C 717 TYR cc_start: 0.7221 (p90) cc_final: 0.6991 (p90) REVERT: E 331 MET cc_start: 0.9067 (mtp) cc_final: 0.8691 (mtp) outliers start: 9 outliers final: 6 residues processed: 89 average time/residue: 0.1243 time to fit residues: 18.6690 Evaluate side-chains 83 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 GLU 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: 5.9990 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: 0.5980 chunk 3 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 686 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.072226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050149 restraints weight = 72268.358| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.68 r_work: 0.2714 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20126 Z= 0.164 Angle : 0.473 7.091 27205 Z= 0.254 Chirality : 0.042 0.174 2968 Planarity : 0.003 0.038 3480 Dihedral : 8.744 164.613 2700 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.73 % Allowed : 6.20 % Favored : 93.07 % 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: 1.18 (0.18), residues: 2347 helix: 2.12 (0.17), residues: 1005 sheet: -0.76 (0.30), residues: 285 loop : -0.00 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 759 TYR 0.016 0.001 TYR A 717 PHE 0.019 0.001 PHE B 763 TRP 0.007 0.001 TRP A 478 HIS 0.006 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00369 (20126) covalent geometry : angle 0.47269 (27205) hydrogen bonds : bond 0.03458 ( 795) hydrogen bonds : angle 4.27399 ( 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 97 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.737 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: 0.7991 (t80) cc_final: 0.7246 (t80) REVERT: A 743 TRP cc_start: 0.4055 (t-100) cc_final: 0.3261 (t-100) REVERT: B 564 ASP cc_start: 0.9206 (t0) cc_final: 0.8997 (t0) REVERT: B 759 ARG cc_start: 0.7385 (mpp-170) cc_final: 0.6820 (mpp-170) REVERT: C 563 ASP cc_start: 0.8374 (p0) cc_final: 0.8139 (p0) REVERT: C 609 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.8957 (m-40) REVERT: C 717 TYR cc_start: 0.7167 (p90) cc_final: 0.6927 (p90) REVERT: D 499 ASP cc_start: 0.9235 (t0) cc_final: 0.8891 (m-30) REVERT: E 331 MET cc_start: 0.9087 (mtp) cc_final: 0.8682 (mtp) REVERT: E 658 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9194 (tp) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 0.1354 time to fit residues: 20.7041 Evaluate side-chains 83 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 D residue 625 LEU Chi-restraints excluded: chain E residue 658 LEU 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: 10.0000 chunk 49 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 6 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3504 r_free = 0.3504 target = 0.072699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050785 restraints weight = 71868.705| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.67 r_work: 0.2734 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20126 Z= 0.114 Angle : 0.444 7.586 27205 Z= 0.241 Chirality : 0.041 0.144 2968 Planarity : 0.003 0.039 3480 Dihedral : 8.460 164.736 2700 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.55 % Allowed : 6.98 % Favored : 92.47 % 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: 1.18 (0.18), residues: 2347 helix: 2.12 (0.17), residues: 1004 sheet: -0.70 (0.30), residues: 296 loop : -0.02 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 759 TYR 0.011 0.001 TYR A 708 PHE 0.034 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 covalent geometry : bond 0.00252 (20126) covalent geometry : angle 0.44447 (27205) hydrogen bonds : bond 0.03230 ( 795) hydrogen bonds : angle 4.17474 ( 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 89 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.766 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 732 TYR cc_start: 0.7951 (t80) cc_final: 0.7196 (t80) REVERT: A 743 TRP cc_start: 0.4071 (t-100) cc_final: 0.3248 (t-100) REVERT: B 564 ASP cc_start: 0.9234 (t0) cc_final: 0.8995 (t0) REVERT: B 697 PHE cc_start: 0.7678 (m-10) cc_final: 0.7373 (m-80) REVERT: B 759 ARG cc_start: 0.7363 (mpp-170) cc_final: 0.6927 (mpp-170) REVERT: C 563 ASP cc_start: 0.8374 (p0) cc_final: 0.8146 (p0) REVERT: C 717 TYR cc_start: 0.7217 (p90) cc_final: 0.6980 (p90) REVERT: D 499 ASP cc_start: 0.9225 (t0) cc_final: 0.8875 (m-30) REVERT: E 331 MET cc_start: 0.9072 (mtp) cc_final: 0.8587 (mtp) REVERT: E 582 THR cc_start: 0.9000 (OUTLIER) cc_final: 0.8777 (p) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1282 time to fit residues: 18.5161 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 : 0.738 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 29 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.073417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.051398 restraints weight = 71417.568| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.71 r_work: 0.2754 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20126 Z= 0.094 Angle : 0.434 8.700 27205 Z= 0.236 Chirality : 0.041 0.190 2968 Planarity : 0.003 0.041 3480 Dihedral : 8.208 167.125 2700 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.68 % Allowed : 7.66 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.18), residues: 2347 helix: 2.15 (0.17), residues: 1003 sheet: -0.66 (0.32), residues: 253 loop : -0.04 (0.19), residues: 1091 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 0.017 0.001 PHE B 763 TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS F 402 Details of bonding type rmsd covalent geometry : bond 0.00203 (20126) covalent geometry : angle 0.43377 (27205) hydrogen bonds : bond 0.02996 ( 795) hydrogen bonds : angle 4.06280 ( 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 92 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.795 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: 0.8369 (mmm) cc_final: 0.7893 (tmm) REVERT: A 732 TYR cc_start: 0.7916 (t80) cc_final: 0.7185 (t80) REVERT: A 743 TRP cc_start: 0.4087 (t-100) cc_final: 0.3227 (t-100) REVERT: B 564 ASP cc_start: 0.9234 (t0) cc_final: 0.8946 (t0) REVERT: B 697 PHE cc_start: 0.7745 (m-10) cc_final: 0.7432 (m-80) REVERT: B 759 ARG cc_start: 0.7399 (mpp-170) cc_final: 0.7054 (mpp-170) REVERT: C 563 ASP cc_start: 0.8358 (p0) cc_final: 0.8119 (p0) REVERT: C 717 TYR cc_start: 0.7249 (p90) cc_final: 0.7019 (p90) REVERT: D 499 ASP cc_start: 0.9247 (t0) cc_final: 0.8933 (m-30) REVERT: E 331 MET cc_start: 0.9076 (mtp) cc_final: 0.8585 (mtp) REVERT: E 582 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8809 (p) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.1294 time to fit residues: 18.9815 Evaluate side-chains 80 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 732 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 567 VAL 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: 3.9990 chunk 220 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 191 optimal weight: 0.0170 chunk 4 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049630 restraints weight = 72362.694| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.65 r_work: 0.2698 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20126 Z= 0.174 Angle : 0.475 8.414 27205 Z= 0.256 Chirality : 0.042 0.161 2968 Planarity : 0.003 0.042 3480 Dihedral : 8.211 170.938 2700 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.82 % Allowed : 8.30 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.18 (0.18), residues: 2347 helix: 2.14 (0.17), residues: 1005 sheet: -0.76 (0.30), residues: 290 loop : -0.03 (0.20), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 597 TYR 0.011 0.001 TYR A 708 PHE 0.057 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 covalent geometry : bond 0.00391 (20126) covalent geometry : angle 0.47528 (27205) hydrogen bonds : bond 0.03455 ( 795) hydrogen bonds : angle 4.23776 ( 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 98 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.676 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 611 MET cc_start: 0.8348 (mmm) cc_final: 0.7967 (tmm) REVERT: A 732 TYR cc_start: 0.7943 (t80) cc_final: 0.7191 (t80) REVERT: A 743 TRP cc_start: 0.4156 (t-100) cc_final: 0.3256 (t-100) REVERT: B 563 ASP cc_start: 0.8390 (p0) cc_final: 0.8066 (p0) REVERT: B 564 ASP cc_start: 0.9304 (t0) cc_final: 0.8917 (t0) REVERT: B 697 PHE cc_start: 0.7835 (m-10) cc_final: 0.7548 (m-80) REVERT: B 759 ARG cc_start: 0.7489 (mpp-170) cc_final: 0.7266 (mpp-170) REVERT: C 563 ASP cc_start: 0.8421 (p0) cc_final: 0.8216 (p0) REVERT: C 609 ASN cc_start: 0.9406 (OUTLIER) cc_final: 0.8990 (m110) REVERT: D 499 ASP cc_start: 0.9265 (t0) cc_final: 0.8966 (m-30) REVERT: E 331 MET cc_start: 0.9106 (mtp) cc_final: 0.8612 (mtp) REVERT: E 477 ARG cc_start: 0.9155 (mmp80) cc_final: 0.8916 (mmp80) REVERT: E 501 MET cc_start: 0.9025 (mtm) cc_final: 0.8800 (mtm) REVERT: E 582 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8790 (p) REVERT: E 658 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9193 (tp) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.1284 time to fit residues: 20.0117 Evaluate side-chains 90 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 732 TYR Chi-restraints excluded: chain B residue 761 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 D residue 625 LEU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 658 LEU 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: 0.8980 chunk 107 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 101 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 321 ASN F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.073049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.051088 restraints weight = 71389.439| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.67 r_work: 0.2743 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20126 Z= 0.094 Angle : 0.442 9.906 27205 Z= 0.240 Chirality : 0.041 0.164 2968 Planarity : 0.003 0.042 3480 Dihedral : 8.025 173.735 2700 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.59 % Allowed : 8.99 % 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: 1.16 (0.18), residues: 2347 helix: 2.11 (0.17), residues: 1003 sheet: -0.70 (0.33), residues: 251 loop : -0.08 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 597 TYR 0.014 0.001 TYR C 717 PHE 0.018 0.001 PHE B 763 TRP 0.006 0.001 TRP C 478 HIS 0.004 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00200 (20126) covalent geometry : angle 0.44179 (27205) hydrogen bonds : bond 0.03049 ( 795) hydrogen bonds : angle 4.07382 ( 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 88 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.640 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: 0.8408 (mmm) cc_final: 0.7897 (tmm) REVERT: A 732 TYR cc_start: 0.7929 (t80) cc_final: 0.7194 (t80) REVERT: A 743 TRP cc_start: 0.4199 (t-100) cc_final: 0.3298 (t-100) REVERT: B 563 ASP cc_start: 0.8378 (p0) cc_final: 0.8057 (p0) REVERT: B 564 ASP cc_start: 0.9281 (t0) cc_final: 0.8865 (t0) REVERT: B 664 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9343 (pt) REVERT: B 697 PHE cc_start: 0.7773 (m-10) cc_final: 0.7469 (m-80) REVERT: C 563 ASP cc_start: 0.8378 (p0) cc_final: 0.8166 (p0) REVERT: D 499 ASP cc_start: 0.9241 (t0) cc_final: 0.8945 (m-30) REVERT: D 658 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9371 (tp) REVERT: E 331 MET cc_start: 0.9089 (mtp) cc_final: 0.8639 (mtp) REVERT: E 582 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8807 (p) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.1278 time to fit residues: 18.2411 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 : 0.812 ------------------------------------------------------------------------------- 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 664 LEU 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 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: 6.9990 chunk 45 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 233 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 205 optimal weight: 0.0870 chunk 196 optimal weight: 9.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3495 r_free = 0.3495 target = 0.072315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050326 restraints weight = 71666.781| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.66 r_work: 0.2719 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20126 Z= 0.143 Angle : 0.466 12.779 27205 Z= 0.251 Chirality : 0.041 0.157 2968 Planarity : 0.003 0.041 3480 Dihedral : 8.064 176.115 2700 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.59 % Allowed : 9.17 % Favored : 90.24 % 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: 1.14 (0.18), residues: 2347 helix: 2.14 (0.17), residues: 1002 sheet: -0.88 (0.30), residues: 283 loop : -0.04 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 597 TYR 0.013 0.001 TYR A 708 PHE 0.074 0.001 PHE A 713 TRP 0.006 0.001 TRP A 478 HIS 0.004 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00322 (20126) covalent geometry : angle 0.46568 (27205) hydrogen bonds : bond 0.03226 ( 795) hydrogen bonds : angle 4.12290 ( 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 88 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.679 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8416 (mmm) cc_final: 0.7942 (tmm) REVERT: A 732 TYR cc_start: 0.7934 (t80) cc_final: 0.7198 (t80) REVERT: A 743 TRP cc_start: 0.4227 (t-100) cc_final: 0.3302 (t-100) REVERT: B 526 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8716 (tp30) REVERT: B 563 ASP cc_start: 0.8406 (p0) cc_final: 0.8089 (p0) REVERT: B 564 ASP cc_start: 0.9304 (t0) cc_final: 0.8901 (t0) REVERT: B 697 PHE cc_start: 0.7790 (m-10) cc_final: 0.7497 (m-80) REVERT: D 499 ASP cc_start: 0.9248 (t0) cc_final: 0.8943 (m-30) REVERT: D 658 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9387 (tp) REVERT: E 331 MET cc_start: 0.9105 (mtp) cc_final: 0.8671 (mtp) REVERT: E 582 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8796 (p) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1254 time to fit residues: 17.6580 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 : 0.726 ------------------------------------------------------------------------------- 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 664 LEU 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 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: 5.9990 chunk 166 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 ASN ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN F 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.070984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.048823 restraints weight = 72306.396| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.63 r_work: 0.2673 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20126 Z= 0.224 Angle : 0.527 12.607 27205 Z= 0.283 Chirality : 0.043 0.161 2968 Planarity : 0.003 0.041 3480 Dihedral : 8.351 177.396 2700 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.59 % Allowed : 9.35 % Favored : 90.05 % 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: 2.04 (0.17), residues: 1004 sheet: -0.79 (0.31), residues: 270 loop : -0.04 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 759 TYR 0.018 0.001 TYR B 717 PHE 0.024 0.001 PHE B 763 TRP 0.007 0.001 TRP A 478 HIS 0.005 0.001 HIS B 737 Details of bonding type rmsd covalent geometry : bond 0.00506 (20126) covalent geometry : angle 0.52685 (27205) hydrogen bonds : bond 0.03713 ( 795) hydrogen bonds : angle 4.36025 ( 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: 13 poor density : 73 time to evaluate : 0.722 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 611 MET cc_start: 0.8407 (mmm) cc_final: 0.7977 (tmm) REVERT: A 732 TYR cc_start: 0.7957 (t80) cc_final: 0.7181 (t80) REVERT: A 743 TRP cc_start: 0.4257 (t-100) cc_final: 0.3317 (t-100) REVERT: B 563 ASP cc_start: 0.8454 (p0) cc_final: 0.8129 (p0) REVERT: B 564 ASP cc_start: 0.9334 (t0) cc_final: 0.8910 (t0) REVERT: B 697 PHE cc_start: 0.7838 (m-10) cc_final: 0.7564 (m-80) REVERT: D 499 ASP cc_start: 0.9242 (t0) cc_final: 0.8952 (m-30) REVERT: D 658 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9409 (tp) REVERT: E 331 MET cc_start: 0.9128 (mtp) cc_final: 0.8663 (mtp) REVERT: E 582 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8752 (p) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.1354 time to fit residues: 18.6049 Evaluate side-chains 84 residues out of total 2196 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 664 LEU Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain B residue 761 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 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 199 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 111 optimal weight: 0.0040 chunk 143 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.050736 restraints weight = 72437.329| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.68 r_work: 0.2753 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20126 Z= 0.094 Angle : 0.459 12.109 27205 Z= 0.247 Chirality : 0.041 0.161 2968 Planarity : 0.003 0.040 3480 Dihedral : 8.092 179.095 2700 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.64 % Allowed : 9.22 % 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: 1.14 (0.18), residues: 2347 helix: 2.11 (0.17), residues: 996 sheet: -0.74 (0.32), residues: 254 loop : -0.07 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 759 TYR 0.014 0.001 TYR C 717 PHE 0.065 0.001 PHE A 713 TRP 0.006 0.001 TRP C 478 HIS 0.004 0.001 HIS F 402 Details of bonding type rmsd covalent geometry : bond 0.00198 (20126) covalent geometry : angle 0.45854 (27205) hydrogen bonds : bond 0.03071 ( 795) hydrogen bonds : angle 4.07275 ( 2262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4278.95 seconds wall clock time: 74 minutes 19.52 seconds (4459.52 seconds total)