Starting phenix.real_space_refine on Fri Jul 3 11:22:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_12804.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_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_2026/7ocd_12804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_12804.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_12804.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_12804.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_12804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ocd_12804/07_2026/7ocd_12804.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'TYR:plan': 1, 'GLU:plan': 22, 'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 3, 'PHE:plan': 1, '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: {'TYR:plan': 1, 'GLU:plan': 22, 'ASP:plan': 10, 'ASN:plan1': 5, 'GLN:plan1': 3, 'PHE:plan': 1, '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: {'GLU:plan': 21, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 13, 'ARG:plan': 7, 'GLN:plan1': 2} 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, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'GLU:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1} 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, 'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 4, 'GLU:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 21, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 13, 'ARG:plan': 7, 'GLN:plan1': 2} 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: 48 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: 48 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: 22 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: 22 Planarities with less than four sites: {'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.28, per 1000 atoms: 0.17 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: 1.07 Conformation dependent library (CDL) restraints added in 511.4 milliseconds 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: 0.37 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: 1.75 Time building geometry restraints manager: 1.32 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: 7213 15.93 - 31.85: 564 31.85 - 47.78: 103 47.78 - 63.70: 40 63.70 - 79.63: 4 Dihedral angle restraints: 7924 sinusoidal: 2436 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 7921 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'B' } 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 12.640 79.627 4404 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (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 ARG 0.010 0.001 ARG C 467 TYR 0.018 0.001 TYR J 119 PHE 0.011 0.001 PHE C 810 TRP 0.007 0.001 TRP D 767 HIS 0.009 0.003 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.34 (13928) covalent geometry : angle 0.70049 / 0.35 (19030) SS BOND : bond 0.00455 / 0.34 ( 8) SS BOND : angle 4.00727 / 2.25 ( 16) hydrogen bonds : bond 0.12819 / 8.58 ( 834) hydrogen bonds : angle 5.49803 / 3.99 ( 2439) *********************** 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 : 0.454 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: 0.0980 time to fit residues: 25.5900 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 : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0070 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3560 r_free = 0.3560 target = 0.106184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.083538 restraints weight = 29698.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.085659 restraints weight = 19246.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.085851 restraints weight = 15490.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086439 restraints weight = 13010.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.086693 restraints weight = 11750.063| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13936 Z= 0.130 Angle : 0.532 8.528 19046 Z= 0.270 Chirality : 0.040 0.141 2270 Planarity : 0.004 0.049 2328 Dihedral : 7.499 58.690 2182 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.12 % Allowed : 7.90 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1880 helix: 2.17 (0.16), residues: 1078 sheet: -2.11 (0.45), residues: 146 loop : -1.32 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 97 TYR 0.011 0.001 TYR C 519 PHE 0.023 0.001 PHE J 32 TRP 0.007 0.001 TRP C 574 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13928) covalent geometry : angle 0.53072 / 0.27 (19030) SS BOND : bond 0.00851 / 0.65 ( 8) SS BOND : angle 1.12758 / 0.64 ( 16) hydrogen bonds : bond 0.03745 / 2.59 ( 834) hydrogen bonds : angle 4.20805 / 3.07 ( 2439) *********************** 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 185 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 701 GLU cc_start: 0.8197 (mp0) cc_final: 0.7590 (mp0) REVERT: C 541 ARG cc_start: 0.8432 (tpp80) cc_final: 0.7941 (tpp-160) REVERT: D 496 MET cc_start: 0.8659 (ttp) cc_final: 0.8400 (ttp) REVERT: D 508 GLN cc_start: 0.8437 (mt0) cc_final: 0.8136 (mt0) REVERT: D 586 ARG cc_start: 0.8370 (mmm-85) cc_final: 0.7770 (mmm160) REVERT: D 709 ASN cc_start: 0.8373 (t0) cc_final: 0.7700 (t0) REVERT: D 715 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.7723 (mmt-90) REVERT: B 496 MET cc_start: 0.8657 (ttp) cc_final: 0.8409 (ttp) REVERT: B 508 GLN cc_start: 0.8439 (mt0) cc_final: 0.8206 (mt0) REVERT: B 709 ASN cc_start: 0.8361 (t0) cc_final: 0.7680 (t0) REVERT: B 715 ARG cc_start: 0.8004 (mmt-90) cc_final: 0.7738 (mmt-90) outliers start: 13 outliers final: 8 residues processed: 178 average time/residue: 0.1139 time to fit residues: 28.6567 Evaluate side-chains 150 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 119 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 171 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3474 r_free = 0.3474 target = 0.100698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.074599 restraints weight = 30629.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.077066 restraints weight = 17441.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078722 restraints weight = 12819.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079579 restraints weight = 10658.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.080266 restraints weight = 9649.645| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13936 Z= 0.279 Angle : 0.625 9.861 19046 Z= 0.321 Chirality : 0.043 0.145 2270 Planarity : 0.004 0.047 2328 Dihedral : 7.509 59.720 2182 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.23 % Allowed : 14.00 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1880 helix: 1.86 (0.16), residues: 1062 sheet: -2.20 (0.43), residues: 146 loop : -1.32 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 97 TYR 0.010 0.002 TYR A 519 PHE 0.013 0.002 PHE B 495 TRP 0.011 0.002 TRP B 578 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00659 / 0.28 (13928) covalent geometry : angle 0.62455 / 0.32 (19030) SS BOND : bond 0.00502 / 0.37 ( 8) SS BOND : angle 1.13180 / 0.67 ( 16) hydrogen bonds : bond 0.04803 / 3.34 ( 834) hydrogen bonds : angle 4.39651 / 3.21 ( 2439) *********************** 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 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.511 Fit side-chains REVERT: A 541 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8080 (tpp80) REVERT: A 701 GLU cc_start: 0.8314 (mp0) cc_final: 0.7641 (mp0) REVERT: C 541 ARG cc_start: 0.8445 (tpp80) cc_final: 0.8004 (tpp80) REVERT: C 701 GLU cc_start: 0.8363 (mp0) cc_final: 0.7804 (mp0) REVERT: D 586 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.7929 (mmm160) REVERT: J 207 PHE cc_start: 0.9060 (m-10) cc_final: 0.8857 (m-80) outliers start: 26 outliers final: 18 residues processed: 171 average time/residue: 0.1095 time to fit residues: 26.8984 Evaluate side-chains 155 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 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 B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU 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 157 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 161 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.077552 restraints weight = 29966.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080208 restraints weight = 16677.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081880 restraints weight = 12120.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082778 restraints weight = 10067.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083479 restraints weight = 9058.337| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13936 Z= 0.135 Angle : 0.512 10.506 19046 Z= 0.258 Chirality : 0.039 0.129 2270 Planarity : 0.003 0.047 2328 Dihedral : 7.200 59.941 2182 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.49 % Allowed : 15.72 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1880 helix: 2.20 (0.16), residues: 1064 sheet: -2.14 (0.44), residues: 140 loop : -1.21 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 97 TYR 0.014 0.001 TYR J 119 PHE 0.009 0.001 PHE J 32 TRP 0.008 0.001 TRP B 766 HIS 0.002 0.000 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13928) covalent geometry : angle 0.51194 / 0.26 (19030) SS BOND : bond 0.00420 / 0.31 ( 8) SS BOND : angle 0.78461 / 0.44 ( 16) hydrogen bonds : bond 0.03759 / 2.62 ( 834) hydrogen bonds : angle 4.00339 / 2.93 ( 2439) *********************** 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 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.486 Fit side-chains REVERT: A 541 ARG cc_start: 0.8257 (tpp80) cc_final: 0.8045 (tpp80) REVERT: A 701 GLU cc_start: 0.8295 (mp0) cc_final: 0.7660 (mp0) REVERT: C 701 GLU cc_start: 0.8262 (mp0) cc_final: 0.7557 (mp0) REVERT: D 408 MET cc_start: 0.7742 (mmt) cc_final: 0.7438 (mmm) REVERT: D 586 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7868 (mmm160) REVERT: D 629 MET cc_start: 0.7649 (mtt) cc_final: 0.7391 (mtt) REVERT: J 199 TYR cc_start: 0.9039 (p90) cc_final: 0.8834 (p90) outliers start: 29 outliers final: 22 residues processed: 172 average time/residue: 0.1026 time to fit residues: 25.8332 Evaluate side-chains 170 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU 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 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 639 LEU Chi-restraints excluded: chain B residue 751 LEU 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 93 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.074073 restraints weight = 31140.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076197 restraints weight = 19180.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077541 restraints weight = 14466.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078346 restraints weight = 12282.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078852 restraints weight = 11178.921| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13936 Z= 0.200 Angle : 0.554 11.441 19046 Z= 0.279 Chirality : 0.040 0.139 2270 Planarity : 0.004 0.044 2328 Dihedral : 7.273 59.874 2182 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.44 % Allowed : 17.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1880 helix: 2.06 (0.16), residues: 1064 sheet: -2.15 (0.44), residues: 140 loop : -1.16 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 97 TYR 0.011 0.001 TYR C 417 PHE 0.019 0.001 PHE J 207 TRP 0.009 0.001 TRP D 767 HIS 0.001 0.001 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (13928) covalent geometry : angle 0.55362 / 0.28 (19030) SS BOND : bond 0.00431 / 0.32 ( 8) SS BOND : angle 0.83592 / 0.48 ( 16) hydrogen bonds : bond 0.04226 / 2.95 ( 834) hydrogen bonds : angle 4.11716 / 3.01 ( 2439) *********************** 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 191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.542 Fit side-chains REVERT: A 395 THR cc_start: 0.8950 (m) cc_final: 0.8719 (m) REVERT: A 701 GLU cc_start: 0.8271 (mp0) cc_final: 0.7526 (mp0) REVERT: C 395 THR cc_start: 0.9153 (m) cc_final: 0.8913 (m) REVERT: C 701 GLU cc_start: 0.8268 (mp0) cc_final: 0.7715 (mp0) REVERT: D 586 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7989 (mmm160) outliers start: 40 outliers final: 29 residues processed: 182 average time/residue: 0.1085 time to fit residues: 29.1558 Evaluate side-chains 175 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 631 SER Chi-restraints excluded: chain D residue 639 LEU 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 145 VAL 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 145 VAL 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 631 SER Chi-restraints excluded: chain B residue 639 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 144 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 104 optimal weight: 0.0570 chunk 150 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3486 r_free = 0.3486 target = 0.101146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079393 restraints weight = 30892.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081014 restraints weight = 22251.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081257 restraints weight = 16979.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081637 restraints weight = 15331.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.081854 restraints weight = 14236.713| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13936 Z= 0.118 Angle : 0.507 11.466 19046 Z= 0.253 Chirality : 0.039 0.148 2270 Planarity : 0.004 0.061 2328 Dihedral : 7.102 59.781 2182 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 18.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1880 helix: 2.32 (0.17), residues: 1064 sheet: -2.16 (0.44), residues: 140 loop : -1.03 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 97 TYR 0.010 0.001 TYR A 417 PHE 0.016 0.001 PHE I 32 TRP 0.007 0.001 TRP D 767 HIS 0.001 0.000 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13928) covalent geometry : angle 0.50662 / 0.25 (19030) SS BOND : bond 0.00341 / 0.26 ( 8) SS BOND : angle 0.64389 / 0.36 ( 16) hydrogen bonds : bond 0.03571 / 2.50 ( 834) hydrogen bonds : angle 3.89150 / 2.85 ( 2439) *********************** 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 189 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.516 Fit side-chains REVERT: A 395 THR cc_start: 0.8823 (m) cc_final: 0.8589 (m) REVERT: A 566 GLU cc_start: 0.7921 (tp30) cc_final: 0.7716 (tp30) REVERT: A 701 GLU cc_start: 0.8191 (mp0) cc_final: 0.7686 (mp0) REVERT: C 395 THR cc_start: 0.8983 (m) cc_final: 0.8745 (m) REVERT: C 701 GLU cc_start: 0.8208 (mp0) cc_final: 0.7615 (mp0) REVERT: D 408 MET cc_start: 0.7587 (mmt) cc_final: 0.7345 (mmm) REVERT: D 586 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.7865 (mmm160) REVERT: B 408 MET cc_start: 0.7634 (mmt) cc_final: 0.7378 (mmm) outliers start: 25 outliers final: 13 residues processed: 183 average time/residue: 0.1086 time to fit residues: 29.1128 Evaluate side-chains 169 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 HIS Chi-restraints excluded: chain A residue 478 THR 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 478 THR Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 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 639 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 166 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 181 optimal weight: 0.0050 chunk 122 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3457 r_free = 0.3457 target = 0.099209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.074999 restraints weight = 31066.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077095 restraints weight = 19266.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.078398 restraints weight = 14611.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078899 restraints weight = 12504.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.079495 restraints weight = 11590.497| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13936 Z= 0.185 Angle : 0.562 11.536 19046 Z= 0.278 Chirality : 0.040 0.139 2270 Planarity : 0.004 0.045 2328 Dihedral : 7.234 59.601 2182 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.09 % Allowed : 18.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1880 helix: 2.20 (0.16), residues: 1064 sheet: -2.19 (0.44), residues: 140 loop : -1.10 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 97 TYR 0.015 0.001 TYR J 119 PHE 0.016 0.001 PHE I 32 TRP 0.010 0.001 TRP D 767 HIS 0.001 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (13928) covalent geometry : angle 0.56142 / 0.28 (19030) SS BOND : bond 0.00376 / 0.28 ( 8) SS BOND : angle 0.71403 / 0.42 ( 16) hydrogen bonds : bond 0.04036 / 2.82 ( 834) hydrogen bonds : angle 3.98986 / 2.93 ( 2439) *********************** 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 196 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.567 Fit side-chains REVERT: A 395 THR cc_start: 0.9067 (m) cc_final: 0.8783 (m) REVERT: A 581 MET cc_start: 0.8602 (tpp) cc_final: 0.7950 (mmm) REVERT: A 701 GLU cc_start: 0.8243 (mp0) cc_final: 0.7722 (mp0) REVERT: C 395 THR cc_start: 0.9243 (m) cc_final: 0.8962 (m) REVERT: C 701 GLU cc_start: 0.8226 (mp0) cc_final: 0.7674 (mp0) REVERT: C 710 GLN cc_start: 0.8233 (mt0) cc_final: 0.8024 (mt0) REVERT: D 586 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7897 (mmm160) REVERT: D 685 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8493 (m) REVERT: D 708 MET cc_start: 0.8582 (tpp) cc_final: 0.8186 (tpt) REVERT: B 685 THR cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (m) REVERT: B 708 MET cc_start: 0.8572 (tpp) cc_final: 0.8168 (tpt) outliers start: 36 outliers final: 23 residues processed: 187 average time/residue: 0.1217 time to fit residues: 33.4282 Evaluate side-chains 180 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 736 THR 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 89 ILE 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 639 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 736 THR 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 41 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.101164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076998 restraints weight = 30590.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079084 restraints weight = 18947.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.080259 restraints weight = 14491.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081189 restraints weight = 12437.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081564 restraints weight = 11237.557| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3071 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 : 0.519 11.534 19046 Z= 0.256 Chirality : 0.039 0.144 2270 Planarity : 0.004 0.054 2328 Dihedral : 7.119 59.959 2182 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.98 % Allowed : 19.50 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1880 helix: 2.36 (0.17), residues: 1066 sheet: -2.17 (0.44), residues: 140 loop : -1.01 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 97 TYR 0.016 0.001 TYR C 669 PHE 0.024 0.001 PHE A 810 TRP 0.008 0.001 TRP B 767 HIS 0.002 0.001 HIS J 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (13928) covalent geometry : angle 0.51891 / 0.26 (19030) SS BOND : bond 0.00256 / 0.17 ( 8) SS BOND : angle 0.65509 / 0.36 ( 16) hydrogen bonds : bond 0.03540 / 2.48 ( 834) hydrogen bonds : angle 3.84848 / 2.82 ( 2439) *********************** 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: 23 poor density : 162 time to evaluate : 0.515 Fit side-chains REVERT: A 395 THR cc_start: 0.9031 (m) cc_final: 0.8804 (m) REVERT: A 581 MET cc_start: 0.8542 (tpp) cc_final: 0.7858 (mmm) REVERT: A 701 GLU cc_start: 0.8176 (mp0) cc_final: 0.7628 (mp0) REVERT: C 395 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8879 (m) REVERT: C 701 GLU cc_start: 0.8160 (mp0) cc_final: 0.7536 (mp0) REVERT: C 710 GLN cc_start: 0.8002 (mt0) cc_final: 0.7787 (mt0) REVERT: D 586 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7884 (mmm160) REVERT: D 708 MET cc_start: 0.8546 (tpp) cc_final: 0.8164 (tpt) REVERT: D 709 ASN cc_start: 0.8841 (t0) cc_final: 0.8368 (t0) REVERT: B 708 MET cc_start: 0.8534 (tpp) cc_final: 0.8148 (tpt) outliers start: 23 outliers final: 19 residues processed: 176 average time/residue: 0.1182 time to fit residues: 30.2347 Evaluate side-chains 175 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 A residue 585 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 431 HIS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 751 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 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 751 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 105 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074501 restraints weight = 31168.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.076476 restraints weight = 19234.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.077821 restraints weight = 14826.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078422 restraints weight = 12564.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.078961 restraints weight = 11543.441| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3126 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= 0.208 Angle : 0.575 12.272 19046 Z= 0.286 Chirality : 0.040 0.149 2270 Planarity : 0.004 0.048 2328 Dihedral : 7.256 59.712 2182 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.92 % Allowed : 19.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1880 helix: 2.19 (0.16), residues: 1066 sheet: -2.16 (0.44), residues: 140 loop : -1.04 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 97 TYR 0.014 0.001 TYR C 417 PHE 0.019 0.001 PHE A 810 TRP 0.011 0.001 TRP D 767 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (13928) covalent geometry : angle 0.57515 / 0.29 (19030) SS BOND : bond 0.00334 / 0.25 ( 8) SS BOND : angle 0.82309 / 0.48 ( 16) hydrogen bonds : bond 0.04180 / 2.91 ( 834) hydrogen bonds : angle 4.00914 / 2.95 ( 2439) *********************** 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 183 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.548 Fit side-chains REVERT: A 395 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8921 (m) REVERT: A 581 MET cc_start: 0.8706 (tpp) cc_final: 0.7993 (mmm) REVERT: A 701 GLU cc_start: 0.8253 (mp0) cc_final: 0.7665 (mp0) REVERT: C 395 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8944 (m) REVERT: C 541 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7800 (tpp80) REVERT: C 701 GLU cc_start: 0.8213 (mp0) cc_final: 0.7639 (mp0) REVERT: C 710 GLN cc_start: 0.8158 (mt0) cc_final: 0.7921 (mt0) REVERT: D 586 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7890 (mmm160) REVERT: B 685 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8460 (m) outliers start: 34 outliers final: 25 residues processed: 170 average time/residue: 0.1253 time to fit residues: 30.9525 Evaluate side-chains 173 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 736 THR 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 89 ILE 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 223 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 736 THR 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 161 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN D 508 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.101001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076837 restraints weight = 30737.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078951 restraints weight = 18882.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080293 restraints weight = 14396.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081146 restraints weight = 12242.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081403 restraints weight = 11091.529| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13936 Z= 0.118 Angle : 0.527 12.335 19046 Z= 0.258 Chirality : 0.038 0.143 2270 Planarity : 0.004 0.065 2328 Dihedral : 6.959 58.981 2182 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.32 % Allowed : 19.59 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.21), residues: 1880 helix: 2.43 (0.17), residues: 1066 sheet: -2.14 (0.44), residues: 140 loop : -0.93 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 97 TYR 0.016 0.001 TYR C 669 PHE 0.019 0.001 PHE A 810 TRP 0.008 0.001 TRP B 767 HIS 0.002 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13928) covalent geometry : angle 0.52676 / 0.26 (19030) SS BOND : bond 0.00305 / 0.23 ( 8) SS BOND : angle 0.61435 / 0.34 ( 16) hydrogen bonds : bond 0.03508 / 2.46 ( 834) hydrogen bonds : angle 3.81666 / 2.81 ( 2439) ********************** 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 184 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.479 Fit side-chains REVERT: A 395 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8845 (m) REVERT: A 701 GLU cc_start: 0.8187 (mp0) cc_final: 0.7640 (mp0) REVERT: C 395 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8858 (m) REVERT: C 541 ARG cc_start: 0.8277 (tpp80) cc_final: 0.7873 (tpp80) REVERT: C 701 GLU cc_start: 0.8122 (mp0) cc_final: 0.7569 (mp0) REVERT: D 586 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7849 (mmm160) REVERT: D 708 MET cc_start: 0.8528 (tpp) cc_final: 0.8141 (tpt) REVERT: B 708 MET cc_start: 0.8428 (tpt) cc_final: 0.8220 (tpt) outliers start: 27 outliers final: 23 residues processed: 175 average time/residue: 0.1249 time to fit residues: 31.6606 Evaluate side-chains 176 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 585 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 736 THR 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 89 ILE 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 631 SER Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 736 THR 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 84 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.0670 chunk 27 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3455 r_free = 0.3455 target = 0.099068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074942 restraints weight = 31276.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.077043 restraints weight = 19239.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078379 restraints weight = 14557.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078963 restraints weight = 12392.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079615 restraints weight = 11397.231| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13936 Z= 0.189 Angle : 0.576 13.324 19046 Z= 0.283 Chirality : 0.040 0.152 2270 Planarity : 0.004 0.059 2328 Dihedral : 7.113 59.728 2182 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.92 % Allowed : 19.07 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1880 helix: 2.28 (0.16), residues: 1068 sheet: -2.17 (0.44), residues: 140 loop : -0.96 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 97 TYR 0.018 0.001 TYR C 417 PHE 0.018 0.001 PHE A 810 TRP 0.012 0.001 TRP D 767 HIS 0.001 0.000 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13928) covalent geometry : angle 0.57541 / 0.28 (19030) SS BOND : bond 0.00345 / 0.26 ( 8) SS BOND : angle 0.73144 / 0.42 ( 16) hydrogen bonds : bond 0.04066 / 2.83 ( 834) hydrogen bonds : angle 3.96054 / 2.91 ( 2439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.58 seconds wall clock time: 37 minutes 34.23 seconds (2254.23 seconds total)