Starting phenix.real_space_refine on Mon Jul 22 21:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/07_2024/7ola_12975_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/07_2024/7ola_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/07_2024/7ola_12975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/07_2024/7ola_12975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/07_2024/7ola_12975_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/07_2024/7ola_12975_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 Residue "A GLU 370": "OE1" <-> "OE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "F PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: 11.24, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 7.96 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.43 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: 6.32 Time building geometry restraints manager: 8.63 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: 98.05 - 105.29: 331 105.29 - 112.53: 10177 112.53 - 119.78: 6781 119.78 - 127.02: 9724 127.02 - 134.26: 192 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 2.520 nonbonded pdb=" OG SER C 579 " pdb=" OD2 ASP D 563 " model vdw 2.210 2.440 nonbonded pdb=" OD1 ASP C 563 " pdb=" N ASP C 564 " model vdw 2.237 2.520 ... (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 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 or r \ esid 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 or resid 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 764 or resid 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 54.340 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.090 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.540 ------------------------------------------------------------------------------- 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= 0.265 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP E 478 HIS 0.004 0.001 HIS F 402 PHE 0.017 0.001 PHE A 713 TYR 0.020 0.001 TYR B 717 ARG 0.002 0.000 ARG A 597 *********************** 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 fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.421 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: 0.2842 time to fit residues: 44.2099 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 30.0000 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 438 ASN C 519 ASN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20126 Z= 0.274 Angle : 0.500 5.816 27205 Z= 0.268 Chirality : 0.043 0.162 2968 Planarity : 0.003 0.034 3480 Dihedral : 10.583 172.850 2700 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.32 % Allowed : 4.84 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2347 helix: 2.11 (0.17), residues: 996 sheet: -0.60 (0.30), residues: 288 loop : -0.00 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 PHE 0.013 0.001 PHE D 545 TYR 0.031 0.001 TYR A 717 ARG 0.003 0.000 ARG A 597 *********************** 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 82 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 2.548 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8083 (t80) cc_final: 0.7408 (t80) REVERT: A 743 TRP cc_start: 0.4148 (t-100) cc_final: 0.3361 (t-100) REVERT: E 331 MET cc_start: 0.8509 (mtp) cc_final: 0.8239 (mtp) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.2901 time to fit residues: 38.4012 Evaluate side-chains 77 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 2.470 ------------------------------------------------------------------------------- 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 119 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 0.5980 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN C 686 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20126 Z= 0.241 Angle : 0.469 7.559 27205 Z= 0.252 Chirality : 0.042 0.158 2968 Planarity : 0.003 0.034 3480 Dihedral : 9.152 163.048 2700 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.59 % Allowed : 6.25 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2347 helix: 2.10 (0.17), residues: 996 sheet: -0.61 (0.30), residues: 288 loop : 0.00 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 PHE 0.029 0.001 PHE A 713 TYR 0.033 0.001 TYR A 717 ARG 0.003 0.000 ARG A 597 *********************** 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 89 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 2.420 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8051 (t80) cc_final: 0.7304 (t80) REVERT: A 743 TRP cc_start: 0.4116 (t-100) cc_final: 0.3264 (t-100) REVERT: E 331 MET cc_start: 0.8504 (mtp) cc_final: 0.8248 (mtp) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.2836 time to fit residues: 40.3267 Evaluate side-chains 82 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP 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 487 ASN 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 212 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1130 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= 0.221 Angle : 0.458 6.940 27205 Z= 0.247 Chirality : 0.041 0.159 2968 Planarity : 0.003 0.036 3480 Dihedral : 8.392 161.855 2700 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.73 % Allowed : 7.34 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2347 helix: 2.12 (0.17), residues: 997 sheet: -0.64 (0.30), residues: 288 loop : 0.02 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 PHE 0.022 0.001 PHE B 735 TYR 0.027 0.001 TYR A 717 ARG 0.003 0.000 ARG A 597 *********************** 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 94 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 2.478 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 611 MET cc_start: 0.8240 (mmm) cc_final: 0.8017 (tmm) REVERT: A 732 TYR cc_start: 0.8055 (t80) cc_final: 0.7299 (t80) REVERT: A 743 TRP cc_start: 0.4171 (t-100) cc_final: 0.3272 (t-100) REVERT: B 564 ASP cc_start: 0.8360 (t0) cc_final: 0.8103 (t70) REVERT: D 499 ASP cc_start: 0.7961 (t0) cc_final: 0.7754 (m-30) REVERT: E 331 MET cc_start: 0.8516 (mtp) cc_final: 0.8201 (mtp) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.2801 time to fit residues: 42.6407 Evaluate side-chains 81 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 525 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20126 Z= 0.149 Angle : 0.438 6.403 27205 Z= 0.237 Chirality : 0.041 0.167 2968 Planarity : 0.003 0.037 3480 Dihedral : 8.113 162.111 2700 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.91 % Allowed : 7.71 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2347 helix: 2.18 (0.17), residues: 997 sheet: -0.67 (0.30), residues: 292 loop : 0.02 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS B 737 PHE 0.038 0.001 PHE A 713 TYR 0.011 0.001 TYR A 708 ARG 0.007 0.000 ARG B 759 *********************** 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 102 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 2.370 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 611 MET cc_start: 0.8268 (mmm) cc_final: 0.7924 (tmm) REVERT: A 732 TYR cc_start: 0.8054 (t80) cc_final: 0.7285 (t80) REVERT: A 743 TRP cc_start: 0.4200 (t-100) cc_final: 0.3265 (t-100) REVERT: C 692 PHE cc_start: 0.8140 (t80) cc_final: 0.7810 (t80) REVERT: E 331 MET cc_start: 0.8514 (mtp) cc_final: 0.8169 (mtp) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.2706 time to fit residues: 44.5909 Evaluate side-chains 85 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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 616 ASP 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 487 ASN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 596 TYR 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 76 optimal weight: 9.9990 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321 ASN E 525 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1319 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= 0.197 Angle : 0.456 8.513 27205 Z= 0.244 Chirality : 0.041 0.142 2968 Planarity : 0.003 0.038 3480 Dihedral : 8.059 164.328 2700 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.73 % Allowed : 9.17 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2347 helix: 2.21 (0.17), residues: 997 sheet: -0.82 (0.29), residues: 299 loop : 0.00 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 478 HIS 0.004 0.001 HIS C 360 PHE 0.025 0.001 PHE B 735 TYR 0.016 0.001 TYR C 717 ARG 0.011 0.000 ARG B 759 *********************** 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 87 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 2.364 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 611 MET cc_start: 0.8254 (mmm) cc_final: 0.7944 (tmm) REVERT: A 732 TYR cc_start: 0.8048 (t80) cc_final: 0.7276 (t80) REVERT: A 743 TRP cc_start: 0.4233 (t-100) cc_final: 0.3286 (t-100) REVERT: C 692 PHE cc_start: 0.8222 (t80) cc_final: 0.7851 (t80) REVERT: E 331 MET cc_start: 0.8535 (mtp) cc_final: 0.8208 (mtp) REVERT: E 611 MET cc_start: 0.8079 (mmm) cc_final: 0.7768 (tpp) outliers start: 16 outliers final: 14 residues processed: 82 average time/residue: 0.2742 time to fit residues: 38.9054 Evaluate side-chains 82 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 2.487 ------------------------------------------------------------------------------- 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 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 0.0870 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 138 optimal weight: 0.0070 chunk 105 optimal weight: 0.9980 overall best weight: 1.0778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** E 321 ASN E 498 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20126 Z= 0.148 Angle : 0.436 8.690 27205 Z= 0.236 Chirality : 0.040 0.137 2968 Planarity : 0.003 0.035 3480 Dihedral : 7.898 166.642 2700 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.96 % Allowed : 9.53 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2347 helix: 2.24 (0.17), residues: 996 sheet: -0.61 (0.30), residues: 276 loop : -0.02 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.004 0.001 HIS B 737 PHE 0.055 0.001 PHE A 713 TYR 0.013 0.001 TYR A 708 ARG 0.006 0.000 ARG B 759 *********************** 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 90 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 2.429 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8035 (t80) cc_final: 0.7265 (t80) REVERT: A 743 TRP cc_start: 0.4274 (t-100) cc_final: 0.3290 (t-100) REVERT: B 664 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9109 (pt) REVERT: C 692 PHE cc_start: 0.8270 (t80) cc_final: 0.7891 (t80) REVERT: D 658 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9178 (tp) REVERT: E 331 MET cc_start: 0.8539 (mtp) cc_final: 0.8310 (mtp) outliers start: 21 outliers final: 14 residues processed: 83 average time/residue: 0.2716 time to fit residues: 39.1147 Evaluate side-chains 83 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 616 ASP 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 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain F residue 320 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 140 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 0.0470 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20126 Z= 0.136 Angle : 0.437 9.102 27205 Z= 0.236 Chirality : 0.040 0.140 2968 Planarity : 0.003 0.037 3480 Dihedral : 7.777 171.491 2700 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.78 % Allowed : 9.72 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2347 helix: 2.27 (0.17), residues: 996 sheet: -0.64 (0.30), residues: 279 loop : -0.06 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 478 HIS 0.003 0.001 HIS B 737 PHE 0.022 0.001 PHE C 735 TYR 0.013 0.001 TYR A 708 ARG 0.005 0.000 ARG B 759 *********************** 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 90 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 2.535 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8011 (t80) cc_final: 0.7290 (t80) REVERT: A 743 TRP cc_start: 0.4287 (t-100) cc_final: 0.3287 (t-100) REVERT: B 664 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9051 (pt) REVERT: B 759 ARG cc_start: 0.7479 (mpp-170) cc_final: 0.6845 (mpp-170) REVERT: C 692 PHE cc_start: 0.8277 (t80) cc_final: 0.7904 (t80) REVERT: D 658 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9178 (tp) REVERT: E 331 MET cc_start: 0.8539 (mtp) cc_final: 0.8306 (mtp) outliers start: 17 outliers final: 14 residues processed: 85 average time/residue: 0.2631 time to fit residues: 38.8525 Evaluate side-chains 88 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 689 VAL 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 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 F residue 320 LEU 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 217 optimal weight: 0.6980 chunk 198 optimal weight: 9.9990 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 191 optimal weight: 0.0010 chunk 200 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1455 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= 0.119 Angle : 0.432 8.693 27205 Z= 0.233 Chirality : 0.040 0.136 2968 Planarity : 0.003 0.036 3480 Dihedral : 7.726 174.842 2700 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.82 % Allowed : 9.99 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 2347 helix: 2.28 (0.17), residues: 996 sheet: -0.66 (0.30), residues: 284 loop : -0.06 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 478 HIS 0.004 0.001 HIS B 737 PHE 0.074 0.001 PHE A 713 TYR 0.013 0.001 TYR C 717 ARG 0.004 0.000 ARG B 759 *********************** 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 91 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 2.599 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7992 (t80) cc_final: 0.7283 (t80) REVERT: A 743 TRP cc_start: 0.4349 (t-100) cc_final: 0.3340 (t-100) REVERT: B 664 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9036 (pt) REVERT: B 759 ARG cc_start: 0.7439 (mpp-170) cc_final: 0.6846 (mpp-170) REVERT: C 692 PHE cc_start: 0.8312 (t80) cc_final: 0.8008 (t80) REVERT: D 658 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9186 (tp) REVERT: E 331 MET cc_start: 0.8545 (mtp) cc_final: 0.8318 (mtp) REVERT: E 611 MET cc_start: 0.7805 (mmm) cc_final: 0.7007 (ttm) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.2876 time to fit residues: 42.3579 Evaluate side-chains 87 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 588 VAL 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 689 VAL Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 470 ILE 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 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 136 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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** E 321 ASN F 358 ASN F 530 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20126 Z= 0.202 Angle : 0.456 8.138 27205 Z= 0.247 Chirality : 0.041 0.137 2968 Planarity : 0.003 0.037 3480 Dihedral : 7.886 177.299 2700 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.82 % Allowed : 10.40 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2347 helix: 2.30 (0.17), residues: 995 sheet: -0.79 (0.30), residues: 283 loop : -0.05 (0.20), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.007 0.001 HIS B 737 PHE 0.033 0.001 PHE B 735 TYR 0.016 0.001 TYR B 717 ARG 0.004 0.000 ARG B 759 ********************** 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 92 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 2.453 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8015 (t80) cc_final: 0.7311 (t80) REVERT: A 743 TRP cc_start: 0.4301 (t-100) cc_final: 0.3289 (t-100) REVERT: B 611 MET cc_start: 0.8187 (mmm) cc_final: 0.7938 (mmm) REVERT: B 759 ARG cc_start: 0.7397 (mpp-170) cc_final: 0.6934 (mpp-170) REVERT: C 692 PHE cc_start: 0.8366 (t80) cc_final: 0.8063 (t80) REVERT: D 658 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9201 (tp) REVERT: E 331 MET cc_start: 0.8529 (mtp) cc_final: 0.8286 (mtp) REVERT: E 611 MET cc_start: 0.7802 (mmm) cc_final: 0.7047 (ttm) outliers start: 18 outliers final: 15 residues processed: 87 average time/residue: 0.2648 time to fit residues: 40.0255 Evaluate side-chains 89 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 732 TYR Chi-restraints excluded: chain C residue 470 ILE 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 F residue 320 LEU 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.2117 > 50: distance: 86 - 110: 24.978 distance: 89 - 107: 25.767 distance: 101 - 107: 27.295 distance: 107 - 108: 7.280 distance: 108 - 109: 14.781 distance: 108 - 111: 11.415 distance: 109 - 110: 14.261 distance: 109 - 116: 17.516 distance: 111 - 112: 14.142 distance: 112 - 113: 30.825 distance: 113 - 114: 21.253 distance: 113 - 115: 8.104 distance: 116 - 117: 27.381 distance: 117 - 118: 28.885 distance: 117 - 120: 42.179 distance: 118 - 119: 34.409 distance: 118 - 122: 23.835 distance: 120 - 121: 34.202 distance: 122 - 123: 4.411 distance: 123 - 124: 20.730 distance: 123 - 126: 21.511 distance: 124 - 133: 5.009 distance: 126 - 127: 40.327 distance: 127 - 128: 28.171 distance: 127 - 129: 16.620 distance: 128 - 130: 5.164 distance: 129 - 131: 8.658 distance: 130 - 132: 12.882 distance: 131 - 132: 4.089 distance: 133 - 134: 40.004 distance: 134 - 135: 43.352 distance: 134 - 137: 40.991 distance: 135 - 136: 56.542 distance: 135 - 140: 60.337 distance: 137 - 138: 16.998 distance: 137 - 139: 26.035 distance: 140 - 141: 44.449 distance: 140 - 146: 55.903 distance: 141 - 142: 6.260 distance: 141 - 144: 3.790 distance: 142 - 143: 11.896 distance: 142 - 147: 9.639 distance: 144 - 145: 45.283 distance: 145 - 146: 23.143 distance: 147 - 148: 37.025 distance: 148 - 149: 29.427 distance: 148 - 151: 20.272 distance: 149 - 150: 7.015 distance: 149 - 155: 10.073 distance: 151 - 152: 21.578 distance: 152 - 153: 7.330 distance: 152 - 154: 6.298 distance: 155 - 156: 31.753 distance: 156 - 157: 33.404 distance: 156 - 159: 34.661 distance: 157 - 158: 48.241 distance: 157 - 167: 40.576 distance: 159 - 160: 9.663 distance: 160 - 161: 31.530 distance: 160 - 162: 27.734 distance: 161 - 163: 31.277 distance: 162 - 164: 28.614 distance: 163 - 165: 8.472 distance: 164 - 165: 39.047 distance: 165 - 166: 26.682 distance: 167 - 168: 11.168 distance: 168 - 169: 44.386 distance: 168 - 171: 14.160 distance: 169 - 170: 25.839 distance: 169 - 175: 18.088 distance: 171 - 172: 7.200 distance: 171 - 173: 24.039 distance: 172 - 174: 26.910 distance: 175 - 176: 12.684 distance: 176 - 177: 31.109 distance: 176 - 179: 16.787 distance: 177 - 178: 35.659 distance: 177 - 186: 40.807 distance: 179 - 180: 19.359 distance: 180 - 181: 36.088 distance: 180 - 182: 28.730 distance: 181 - 183: 21.419 distance: 182 - 184: 22.938 distance: 183 - 185: 25.286 distance: 184 - 185: 9.029 distance: 186 - 187: 38.826 distance: 187 - 188: 5.501 distance: 187 - 190: 14.779 distance: 188 - 189: 30.164 distance: 188 - 193: 18.963 distance: 190 - 191: 37.381 distance: 190 - 192: 36.371