Starting phenix.real_space_refine on Thu Jul 31 22:24:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ocd_12804/07_2025/7ocd_12804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ocd_12804/07_2025/7ocd_12804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2025/7ocd_12804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2025/7ocd_12804.map" model { file = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2025/7ocd_12804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2025/7ocd_12804.cif" } resolution = 3.5 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= 0.002 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 8982 2.51 5 N 2194 2.21 5 O 2366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13624 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2773 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 381} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2773 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 381} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 400 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 22, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 203 Chain: "D" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2777 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "I" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1153 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1153 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 2777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2777 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 180 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'E2Q': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Unusual residues: {'E2Q': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'E2Q': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'E2Q': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 12.96, per 1000 atoms: 0.95 Number of scatterers: 13624 At special positions: 0 Unit cell: (129.47, 110.21, 131.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 2366 8.00 N 2194 7.00 C 8982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3496 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 19 sheets defined 57.4% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.700A pdb=" N ASP A 415 " --> pdb=" O GLU A 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 485 removed outlier: 3.655A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.537A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 623 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 649 through 657 Processing helix chain 'A' and resid 660 through 672 removed outlier: 3.565A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.724A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.675A pdb=" N ASP C 415 " --> pdb=" O GLU C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.652A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.552A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 542 removed outlier: 3.511A pdb=" N PHE C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 623 Processing helix chain 'C' and resid 631 through 637 removed outlier: 3.502A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 657 Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.566A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 702 through 709 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.752A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER C 814 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.584A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.518A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.543A pdb=" N LEU D 639 " --> pdb=" O SER D 635 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.531A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 758 through 768 Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.589A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 41 Processing helix chain 'I' and resid 118 through 127 Processing helix chain 'I' and resid 128 through 150 Processing helix chain 'I' and resid 156 through 184 removed outlier: 3.918A pdb=" N GLY I 160 " --> pdb=" O ASN I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 231 removed outlier: 3.666A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 41 Processing helix chain 'J' and resid 118 through 127 Processing helix chain 'J' and resid 128 through 150 Processing helix chain 'J' and resid 156 through 184 removed outlier: 3.918A pdb=" N GLY J 160 " --> pdb=" O ASN J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 231 removed outlier: 3.666A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.584A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.518A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.543A pdb=" N LEU B 639 " --> pdb=" O SER B 635 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.531A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 788 through 819 removed outlier: 3.589A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 440 removed outlier: 5.387A pdb=" N VAL A 393 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 470 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 494 removed outlier: 3.673A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 494 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.394A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 700 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 437 through 440 removed outlier: 5.384A pdb=" N VAL C 393 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 470 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AA7, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AA8, first strand: chain 'C' and resid 492 through 494 removed outlier: 3.692A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 494 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.398A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 700 " --> pdb=" O SER C 497 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 398 through 399 Processing sheet with id=AB2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB3, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.566A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 704 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 90 through 91 removed outlier: 3.894A pdb=" N CYS I 90 " --> pdb=" O HIS I 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 90 through 91 removed outlier: 3.894A pdb=" N CYS J 90 " --> pdb=" O HIS J 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AB8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.565A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 704 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2439 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: 4.35 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2056 1.31 - 1.43: 3969 1.43 - 1.56: 7773 1.56 - 1.68: 4 1.68 - 1.81: 126 Bond restraints: 13928 Sorted by residual: bond pdb=" C09 E2Q A 901 " pdb=" S11 E2Q A 901 " ideal model delta sigma weight residual 1.799 1.691 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C09 E2Q C 901 " pdb=" S11 E2Q C 901 " ideal model delta sigma weight residual 1.799 1.694 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C09 E2Q D 901 " pdb=" S11 E2Q D 901 " ideal model delta sigma weight residual 1.799 1.699 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C09 E2Q B 901 " pdb=" S11 E2Q B 901 " ideal model delta sigma weight residual 1.799 1.699 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C21 PC1 C 903 " pdb=" O21 PC1 C 903 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 13923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 18506 1.80 - 3.61: 398 3.61 - 5.41: 106 5.41 - 7.21: 12 7.21 - 9.01: 8 Bond angle restraints: 19030 Sorted by residual: angle pdb=" C22 PC1 A 903 " pdb=" C21 PC1 A 903 " pdb=" O21 PC1 A 903 " ideal model delta sigma weight residual 111.12 120.13 -9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" C22 PC1 C 903 " pdb=" C21 PC1 C 903 " pdb=" O21 PC1 C 903 " ideal model delta sigma weight residual 111.12 120.11 -8.99 3.00e+00 1.11e-01 8.97e+00 angle pdb=" C22 PC1 C 902 " pdb=" C21 PC1 C 902 " pdb=" O21 PC1 C 902 " ideal model delta sigma weight residual 111.12 119.96 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" C22 PC1 A 902 " pdb=" C21 PC1 A 902 " pdb=" O21 PC1 A 902 " ideal model delta sigma weight residual 111.12 119.96 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" C32 PC1 D 902 " pdb=" C31 PC1 D 902 " pdb=" O31 PC1 D 902 " ideal model delta sigma weight residual 111.44 119.95 -8.51 3.00e+00 1.11e-01 8.05e+00 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 7217 15.93 - 31.85: 564 31.85 - 47.78: 103 47.78 - 63.70: 44 63.70 - 79.63: 4 Dihedral angle restraints: 7932 sinusoidal: 2444 harmonic: 5488 Sorted by residual: dihedral pdb=" CB CYS C 714 " pdb=" SG CYS C 714 " pdb=" SG CYS C 769 " pdb=" CB CYS C 769 " ideal model delta sinusoidal sigma weight residual 93.00 161.07 -68.07 1 1.00e+01 1.00e-02 6.01e+01 dihedral pdb=" CB CYS A 714 " pdb=" SG CYS A 714 " pdb=" SG CYS A 769 " pdb=" CB CYS A 769 " ideal model delta sinusoidal sigma weight residual 93.00 160.30 -67.30 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual 93.00 138.96 -45.96 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 7929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1243 0.027 - 0.055: 619 0.055 - 0.082: 299 0.082 - 0.109: 81 0.109 - 0.137: 28 Chirality restraints: 2270 Sorted by residual: chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA VAL D 406 " pdb=" N VAL D 406 " pdb=" C VAL D 406 " pdb=" CB VAL D 406 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 406 " pdb=" N VAL B 406 " pdb=" C VAL B 406 " pdb=" CB VAL B 406 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2267 not shown) Planarity restraints: 2328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 515 " 0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 516 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 119 " 0.013 2.00e-02 2.50e+03 8.70e-03 1.51e+00 pdb=" CG TYR I 119 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR I 119 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR I 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR I 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR I 119 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 119 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR I 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 119 " -0.013 2.00e-02 2.50e+03 8.66e-03 1.50e+00 pdb=" CG TYR J 119 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR J 119 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR J 119 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 119 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR J 119 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR J 119 " -0.009 2.00e-02 2.50e+03 ... (remaining 2325 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 282 2.69 - 3.24: 14300 3.24 - 3.79: 22018 3.79 - 4.35: 26319 4.35 - 4.90: 45569 Nonbonded interactions: 108488 Sorted by model distance: nonbonded pdb=" N14 E2Q A 901 " pdb=" O16 E2Q A 901 " model vdw 2.132 3.120 nonbonded pdb=" N14 E2Q C 901 " pdb=" O16 E2Q C 901 " model vdw 2.135 3.120 nonbonded pdb=" OD2 ASP C 586 " pdb=" OG SER D 592 " model vdw 2.138 3.040 nonbonded pdb=" N14 E2Q B 901 " pdb=" O16 E2Q B 901 " model vdw 2.140 3.120 nonbonded pdb=" N14 E2Q D 901 " pdb=" O16 E2Q D 901 " model vdw 2.140 3.120 ... (remaining 108483 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 62.320 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.470 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.108 13936 Z= 0.335 Angle : 0.710 9.549 19046 Z= 0.353 Chirality : 0.040 0.137 2270 Planarity : 0.003 0.036 2328 Dihedral : 12.732 79.627 4412 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.37 (0.20), residues: 1880 helix: 1.77 (0.16), residues: 1068 sheet: -2.21 (0.44), residues: 146 loop : -1.77 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 767 HIS 0.009 0.003 HIS A 431 PHE 0.011 0.001 PHE C 810 TYR 0.018 0.001 TYR J 119 ARG 0.010 0.001 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.12819 ( 834) hydrogen bonds : angle 5.49803 ( 2439) SS BOND : bond 0.00455 ( 8) SS BOND : angle 4.00727 ( 16) covalent geometry : bond 0.00767 (13928) covalent geometry : angle 0.70049 (19030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 1.528 Fit side-chains REVERT: A 701 GLU cc_start: 0.7997 (mp0) cc_final: 0.7683 (mp0) REVERT: C 701 GLU cc_start: 0.8047 (mp0) cc_final: 0.7644 (mp0) REVERT: D 496 MET cc_start: 0.8738 (ttp) cc_final: 0.8535 (ttp) REVERT: D 586 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7479 (ttp80) REVERT: D 709 ASN cc_start: 0.8197 (t0) cc_final: 0.7797 (t0) REVERT: B 496 MET cc_start: 0.8734 (ttp) cc_final: 0.8534 (ttp) REVERT: B 709 ASN cc_start: 0.8160 (t0) cc_final: 0.7748 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3564 time to fit residues: 92.9740 Evaluate side-chains 138 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.0770 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 0.0030 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 0.4548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 83 HIS ** 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 = 0.3579 r_free = 0.3579 target = 0.107464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085190 restraints weight = 29335.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085890 restraints weight = 21418.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.086476 restraints weight = 15603.314| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13936 Z= 0.115 Angle : 0.522 8.251 19046 Z= 0.264 Chirality : 0.039 0.139 2270 Planarity : 0.004 0.048 2328 Dihedral : 7.499 59.918 2190 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.95 % Allowed : 7.99 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.07 (0.21), residues: 1880 helix: 2.27 (0.16), residues: 1076 sheet: -2.12 (0.45), residues: 146 loop : -1.31 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.002 0.001 HIS J 83 PHE 0.022 0.001 PHE J 32 TYR 0.011 0.001 TYR C 519 ARG 0.009 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 834) hydrogen bonds : angle 4.14433 ( 2439) SS BOND : bond 0.00407 ( 8) SS BOND : angle 1.05165 ( 16) covalent geometry : bond 0.00250 (13928) covalent geometry : angle 0.52104 (19030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 541 ARG cc_start: 0.8404 (tpp80) cc_final: 0.7930 (tpp-160) REVERT: D 496 MET cc_start: 0.8590 (ttp) cc_final: 0.8350 (ttp) REVERT: D 508 GLN cc_start: 0.8420 (mt0) cc_final: 0.8203 (mt0) REVERT: D 586 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7744 (mmm160) REVERT: D 709 ASN cc_start: 0.8253 (t0) cc_final: 0.7624 (t0) REVERT: B 496 MET cc_start: 0.8614 (ttp) cc_final: 0.8375 (ttp) REVERT: B 508 GLN cc_start: 0.8412 (mt0) cc_final: 0.8193 (mt0) REVERT: B 709 ASN cc_start: 0.8230 (t0) cc_final: 0.7600 (t0) outliers start: 11 outliers final: 8 residues processed: 183 average time/residue: 0.3404 time to fit residues: 88.5298 Evaluate side-chains 154 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 628 ARG Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 184 optimal weight: 0.1980 chunk 177 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** 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 = 0.3484 r_free = 0.3484 target = 0.101309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.075306 restraints weight = 30344.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.077798 restraints weight = 17136.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079450 restraints weight = 12595.431| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13936 Z= 0.273 Angle : 0.612 8.553 19046 Z= 0.315 Chirality : 0.042 0.146 2270 Planarity : 0.004 0.046 2328 Dihedral : 7.502 59.568 2190 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.23 % Allowed : 13.75 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.73 (0.20), residues: 1880 helix: 1.93 (0.16), residues: 1064 sheet: -2.21 (0.43), residues: 146 loop : -1.28 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 578 HIS 0.002 0.001 HIS J 83 PHE 0.013 0.002 PHE D 495 TYR 0.013 0.002 TYR D 647 ARG 0.008 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 834) hydrogen bonds : angle 4.34776 ( 2439) SS BOND : bond 0.00513 ( 8) SS BOND : angle 1.07737 ( 16) covalent geometry : bond 0.00649 (13928) covalent geometry : angle 0.61156 (19030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 2.146 Fit side-chains REVERT: A 541 ARG cc_start: 0.8370 (tpp80) cc_final: 0.8065 (tpp80) REVERT: A 701 GLU cc_start: 0.8342 (mp0) cc_final: 0.7639 (mp0) REVERT: C 541 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7983 (tpp80) REVERT: C 701 GLU cc_start: 0.8349 (mp0) cc_final: 0.7758 (mp0) REVERT: D 586 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.7901 (mmm160) outliers start: 26 outliers final: 17 residues processed: 169 average time/residue: 0.3300 time to fit residues: 80.8731 Evaluate side-chains 155 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.104172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.078406 restraints weight = 29719.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081043 restraints weight = 16520.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.082711 restraints weight = 12024.429| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13936 Z= 0.126 Angle : 0.505 10.418 19046 Z= 0.254 Chirality : 0.039 0.126 2270 Planarity : 0.003 0.046 2328 Dihedral : 7.184 59.996 2190 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.89 % Allowed : 15.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.14 (0.20), residues: 1880 helix: 2.29 (0.16), residues: 1064 sheet: -2.09 (0.45), residues: 140 loop : -1.17 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 766 HIS 0.002 0.000 HIS J 83 PHE 0.020 0.001 PHE J 207 TYR 0.015 0.001 TYR J 119 ARG 0.009 0.001 ARG J 97 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 834) hydrogen bonds : angle 3.95307 ( 2439) SS BOND : bond 0.00392 ( 8) SS BOND : angle 0.72628 ( 16) covalent geometry : bond 0.00289 (13928) covalent geometry : angle 0.50484 (19030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.507 Fit side-chains REVERT: A 541 ARG cc_start: 0.8219 (tpp80) cc_final: 0.8018 (tpp80) REVERT: A 701 GLU cc_start: 0.8252 (mp0) cc_final: 0.7630 (mp0) REVERT: C 701 GLU cc_start: 0.8280 (mp0) cc_final: 0.7591 (mp0) REVERT: D 586 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.7881 (mmm160) outliers start: 22 outliers final: 12 residues processed: 173 average time/residue: 0.3221 time to fit residues: 79.2325 Evaluate side-chains 160 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.074285 restraints weight = 31086.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076343 restraints weight = 19013.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077651 restraints weight = 14498.766| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13936 Z= 0.209 Angle : 0.561 10.559 19046 Z= 0.283 Chirality : 0.040 0.140 2270 Planarity : 0.004 0.043 2328 Dihedral : 7.341 59.695 2190 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.41 % Allowed : 17.70 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 0.96 (0.20), residues: 1880 helix: 2.09 (0.16), residues: 1064 sheet: -2.12 (0.44), residues: 140 loop : -1.14 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 578 HIS 0.002 0.001 HIS J 83 PHE 0.014 0.001 PHE J 207 TYR 0.014 0.001 TYR I 119 ARG 0.011 0.001 ARG J 97 Details of bonding type rmsd hydrogen bonds : bond 0.04259 ( 834) hydrogen bonds : angle 4.11198 ( 2439) SS BOND : bond 0.00426 ( 8) SS BOND : angle 0.84461 ( 16) covalent geometry : bond 0.00495 (13928) covalent geometry : angle 0.56087 (19030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 1.530 Fit side-chains REVERT: A 701 GLU cc_start: 0.8275 (mp0) cc_final: 0.7675 (mp0) REVERT: C 541 ARG cc_start: 0.8458 (tpp-160) cc_final: 0.7146 (tpp-160) REVERT: C 701 GLU cc_start: 0.8257 (mp0) cc_final: 0.7690 (mp0) REVERT: D 586 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7783 (mmm160) outliers start: 28 outliers final: 19 residues processed: 169 average time/residue: 0.3274 time to fit residues: 79.5719 Evaluate side-chains 161 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 162 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079418 restraints weight = 31034.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.080996 restraints weight = 22409.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081225 restraints weight = 17291.335| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13936 Z= 0.124 Angle : 0.513 10.976 19046 Z= 0.257 Chirality : 0.039 0.151 2270 Planarity : 0.004 0.049 2328 Dihedral : 7.192 59.980 2190 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.66 % Allowed : 18.04 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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 (0.21), residues: 1880 helix: 2.37 (0.17), residues: 1064 sheet: -2.11 (0.45), residues: 140 loop : -1.03 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 767 HIS 0.002 0.000 HIS J 83 PHE 0.016 0.001 PHE I 32 TYR 0.015 0.001 TYR A 669 ARG 0.011 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 834) hydrogen bonds : angle 3.90146 ( 2439) SS BOND : bond 0.00339 ( 8) SS BOND : angle 0.65311 ( 16) covalent geometry : bond 0.00287 (13928) covalent geometry : angle 0.51329 (19030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.452 Fit side-chains REVERT: A 395 THR cc_start: 0.9086 (m) cc_final: 0.8815 (m) REVERT: A 541 ARG cc_start: 0.7093 (tpp80) cc_final: 0.6839 (mmt180) REVERT: A 701 GLU cc_start: 0.8200 (mp0) cc_final: 0.7708 (mp0) REVERT: C 701 GLU cc_start: 0.8255 (mp0) cc_final: 0.7604 (mp0) REVERT: D 586 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7580 (mmm160) outliers start: 31 outliers final: 17 residues processed: 184 average time/residue: 0.2824 time to fit residues: 74.9417 Evaluate side-chains 170 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 117 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.100751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076462 restraints weight = 30866.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078607 restraints weight = 18923.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.079940 restraints weight = 14395.657| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13936 Z= 0.135 Angle : 0.532 11.178 19046 Z= 0.261 Chirality : 0.039 0.138 2270 Planarity : 0.004 0.049 2328 Dihedral : 7.198 59.761 2190 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.49 % Allowed : 18.56 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.33 (0.21), residues: 1880 helix: 2.44 (0.17), residues: 1064 sheet: -2.08 (0.45), residues: 140 loop : -1.04 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 767 HIS 0.002 0.000 HIS J 83 PHE 0.017 0.001 PHE I 32 TYR 0.016 0.001 TYR A 669 ARG 0.012 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 834) hydrogen bonds : angle 3.88331 ( 2439) SS BOND : bond 0.00330 ( 8) SS BOND : angle 0.60071 ( 16) covalent geometry : bond 0.00315 (13928) covalent geometry : angle 0.53151 (19030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.470 Fit side-chains REVERT: A 395 THR cc_start: 0.9037 (m) cc_final: 0.8749 (m) REVERT: A 581 MET cc_start: 0.8541 (tpp) cc_final: 0.7895 (mmm) REVERT: A 701 GLU cc_start: 0.8197 (mp0) cc_final: 0.7644 (mp0) REVERT: C 701 GLU cc_start: 0.8243 (mp0) cc_final: 0.7572 (mp0) REVERT: D 586 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7748 (mmm160) REVERT: D 629 MET cc_start: 0.7851 (mmm) cc_final: 0.7390 (ttm) REVERT: B 629 MET cc_start: 0.7856 (mmm) cc_final: 0.7424 (ttm) REVERT: B 708 MET cc_start: 0.8528 (tpp) cc_final: 0.8147 (tpt) outliers start: 29 outliers final: 16 residues processed: 181 average time/residue: 0.2774 time to fit residues: 72.1349 Evaluate side-chains 165 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 64 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 148 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.101039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076816 restraints weight = 30746.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.078950 restraints weight = 18802.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.080266 restraints weight = 14290.054| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13936 Z= 0.123 Angle : 0.511 11.630 19046 Z= 0.252 Chirality : 0.038 0.136 2270 Planarity : 0.004 0.054 2328 Dihedral : 7.148 59.839 2190 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 18.99 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.44 (0.21), residues: 1880 helix: 2.52 (0.17), residues: 1068 sheet: -2.08 (0.45), residues: 140 loop : -0.98 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 767 HIS 0.001 0.000 HIS J 105 PHE 0.014 0.001 PHE B 814 TYR 0.017 0.001 TYR C 669 ARG 0.014 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 834) hydrogen bonds : angle 3.80677 ( 2439) SS BOND : bond 0.00328 ( 8) SS BOND : angle 0.57905 ( 16) covalent geometry : bond 0.00283 (13928) covalent geometry : angle 0.51063 (19030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.585 Fit side-chains REVERT: A 395 THR cc_start: 0.9039 (m) cc_final: 0.8772 (m) REVERT: A 541 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7245 (tpp-160) REVERT: A 581 MET cc_start: 0.8554 (tpp) cc_final: 0.7863 (mmm) REVERT: A 701 GLU cc_start: 0.8187 (mp0) cc_final: 0.7625 (mp0) REVERT: C 701 GLU cc_start: 0.8234 (mp0) cc_final: 0.7499 (mp0) REVERT: C 704 MET cc_start: 0.8543 (tpp) cc_final: 0.8311 (tpp) REVERT: D 586 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7753 (mmm160) REVERT: D 629 MET cc_start: 0.7869 (mmm) cc_final: 0.7492 (ttm) REVERT: B 629 MET cc_start: 0.7861 (mmm) cc_final: 0.7514 (ttm) REVERT: B 708 MET cc_start: 0.8488 (tpp) cc_final: 0.8151 (tpt) outliers start: 25 outliers final: 18 residues processed: 176 average time/residue: 0.2846 time to fit residues: 71.8496 Evaluate side-chains 168 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 153 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 170 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.075130 restraints weight = 30808.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077193 restraints weight = 19079.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.078492 restraints weight = 14582.062| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13936 Z= 0.185 Angle : 0.559 12.051 19046 Z= 0.278 Chirality : 0.040 0.146 2270 Planarity : 0.004 0.055 2328 Dihedral : 7.314 59.659 2190 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.89 % Allowed : 19.07 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.29 (0.20), residues: 1880 helix: 2.37 (0.16), residues: 1066 sheet: -2.14 (0.44), residues: 140 loop : -0.99 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 767 HIS 0.001 0.000 HIS J 83 PHE 0.012 0.001 PHE D 495 TYR 0.015 0.001 TYR A 669 ARG 0.014 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 834) hydrogen bonds : angle 3.96349 ( 2439) SS BOND : bond 0.00318 ( 8) SS BOND : angle 0.75060 ( 16) covalent geometry : bond 0.00441 (13928) covalent geometry : angle 0.55928 (19030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.493 Fit side-chains REVERT: A 395 THR cc_start: 0.9201 (m) cc_final: 0.8966 (m) REVERT: A 581 MET cc_start: 0.8700 (tpp) cc_final: 0.7976 (mmm) REVERT: A 701 GLU cc_start: 0.8201 (mp0) cc_final: 0.7626 (mp0) REVERT: C 541 ARG cc_start: 0.8315 (tpp80) cc_final: 0.7851 (tpp80) REVERT: C 701 GLU cc_start: 0.8224 (mp0) cc_final: 0.7601 (mp0) REVERT: D 586 ARG cc_start: 0.8218 (mmm-85) cc_final: 0.7774 (mmm160) REVERT: D 629 MET cc_start: 0.7961 (mmm) cc_final: 0.7589 (ttm) REVERT: B 496 MET cc_start: 0.8902 (ttp) cc_final: 0.8595 (ttp) REVERT: B 629 MET cc_start: 0.7970 (mmm) cc_final: 0.7621 (ttm) outliers start: 22 outliers final: 19 residues processed: 162 average time/residue: 0.2954 time to fit residues: 67.8602 Evaluate side-chains 166 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain J residue 218 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 141 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 0.0370 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 113 optimal weight: 0.0470 chunk 61 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN D 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.102019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.080666 restraints weight = 30771.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080325 restraints weight = 30905.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.081268 restraints weight = 21682.999| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13936 Z= 0.104 Angle : 0.509 12.138 19046 Z= 0.250 Chirality : 0.038 0.140 2270 Planarity : 0.004 0.065 2328 Dihedral : 7.048 59.661 2190 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.37 % Allowed : 19.85 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.50 (0.21), residues: 1880 helix: 2.57 (0.17), residues: 1070 sheet: -2.07 (0.45), residues: 140 loop : -0.98 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 605 HIS 0.001 0.000 HIS J 83 PHE 0.024 0.001 PHE A 810 TYR 0.017 0.001 TYR A 669 ARG 0.016 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 834) hydrogen bonds : angle 3.75631 ( 2439) SS BOND : bond 0.00280 ( 8) SS BOND : angle 0.53858 ( 16) covalent geometry : bond 0.00232 (13928) covalent geometry : angle 0.50914 (19030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.505 Fit side-chains REVERT: A 395 THR cc_start: 0.8973 (m) cc_final: 0.8695 (m) REVERT: A 701 GLU cc_start: 0.8077 (mp0) cc_final: 0.7563 (mp0) REVERT: C 541 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7907 (tpp80) REVERT: C 701 GLU cc_start: 0.8209 (mp0) cc_final: 0.7563 (mp0) REVERT: D 586 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7701 (mmm160) REVERT: D 629 MET cc_start: 0.7971 (mmm) cc_final: 0.7566 (ttm) REVERT: D 708 MET cc_start: 0.8404 (tpp) cc_final: 0.8034 (tpt) REVERT: D 709 ASN cc_start: 0.8716 (t0) cc_final: 0.8278 (t0) REVERT: B 496 MET cc_start: 0.8769 (ttp) cc_final: 0.8495 (ttp) REVERT: B 629 MET cc_start: 0.7976 (mmm) cc_final: 0.7588 (ttm) outliers start: 16 outliers final: 13 residues processed: 171 average time/residue: 0.2869 time to fit residues: 69.8089 Evaluate side-chains 162 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 751 LEU Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 223 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 789 LEU Chi-restraints excluded: chain B residue 807 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN B 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073580 restraints weight = 31266.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075579 restraints weight = 19353.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.076803 restraints weight = 14798.794| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13936 Z= 0.278 Angle : 0.634 13.539 19046 Z= 0.317 Chirality : 0.042 0.149 2270 Planarity : 0.004 0.056 2328 Dihedral : 7.477 58.633 2190 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.63 % Allowed : 20.45 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: 1.08 (0.20), residues: 1880 helix: 2.14 (0.16), residues: 1070 sheet: -2.19 (0.45), residues: 140 loop : -1.00 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 767 HIS 0.001 0.000 HIS C 431 PHE 0.031 0.002 PHE I 165 TYR 0.013 0.002 TYR A 669 ARG 0.015 0.001 ARG I 97 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 834) hydrogen bonds : angle 4.14951 ( 2439) SS BOND : bond 0.00370 ( 8) SS BOND : angle 0.90809 ( 16) covalent geometry : bond 0.00662 (13928) covalent geometry : angle 0.63419 (19030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4795.61 seconds wall clock time: 86 minutes 40.31 seconds (5200.31 seconds total)