Starting phenix.real_space_refine on Tue Dec 31 20:21:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8aym_15716/12_2024/8aym_15716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aym_15716/12_2024/8aym_15716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8aym_15716/12_2024/8aym_15716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aym_15716/12_2024/8aym_15716.map" model { file = "/net/cci-nas-00/data/ceres_data/8aym_15716/12_2024/8aym_15716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aym_15716/12_2024/8aym_15716.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 10 5.49 5 S 92 5.16 5 Cl 2 4.86 5 C 10462 2.51 5 N 2506 2.21 5 O 2872 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15962 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1358 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3103 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3103 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 391} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3168 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "J" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1358 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PLM': 1, 'XVD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'PLM': 4, 'POV': 2, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 126 Unusual residues: {'OLC': 1, 'PLM': 2, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 126 Unusual residues: {'OLC': 1, 'PLM': 2, 'POV': 1, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'PLM': 4, 'POV': 2, 'ZK1': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PLM': 1, 'XVD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.33, per 1000 atoms: 0.65 Number of scatterers: 15962 At special positions: 0 Unit cell: (131.61, 110.21, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 92 16.00 P 10 15.00 F 18 9.00 O 2872 8.00 N 2506 7.00 C 10462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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=2.03 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 B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.42 Conformation dependent library (CDL) restraints added in 2.0 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 22 sheets defined 55.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'I' and resid 19 through 40 Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 128 through 150 removed outlier: 3.962A pdb=" N VAL I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 184 removed outlier: 3.579A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY I 169 " --> pdb=" O PHE I 165 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR I 179 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 184 " --> pdb=" O ILE I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 233 removed outlier: 4.183A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.637A 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 457 through 465 Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.850A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 543 through 548 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 625 Processing helix chain 'C' and resid 631 through 638 removed outlier: 3.926A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 658 removed outlier: 3.955A pdb=" N GLU C 653 " --> pdb=" O GLY C 649 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 673 removed outlier: 3.560A pdb=" N LYS C 671 " --> pdb=" O TRP C 667 " (cutoff:3.500A) removed outlier: 3.591A 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 710 Processing helix chain 'C' and resid 738 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 788 through 815 removed outlier: 3.838A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 4.376A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.861A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.647A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 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 636 through 642 removed outlier: 3.912A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.583A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 4.325A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 776 through 780 removed outlier: 3.525A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.853A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 4.366A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.862A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.638A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 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 636 through 642 removed outlier: 3.917A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.585A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 4.307A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.526A pdb=" N GLY B 779 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.851A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 removed outlier: 3.637A 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 457 through 465 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.848A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 625 Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.906A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 removed outlier: 3.955A pdb=" N GLU A 653 " --> pdb=" O GLY A 649 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.559A pdb=" N LYS A 671 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 3.590A 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 710 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.839A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 40 Processing helix chain 'J' and resid 115 through 128 Processing helix chain 'J' and resid 128 through 150 removed outlier: 3.962A pdb=" N VAL J 150 " --> pdb=" O ALA J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 184 removed outlier: 3.580A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY J 169 " --> pdb=" O PHE J 165 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR J 179 " --> pdb=" O GLY J 175 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA J 184 " --> pdb=" O ILE J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 233 removed outlier: 4.183A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 45 through 46 Processing sheet with id=AA2, first strand: chain 'I' and resid 88 through 90 Processing sheet with id=AA3, first strand: chain 'C' and resid 391 through 392 removed outlier: 6.402A pdb=" N TYR C 391 " --> pdb=" O ARG C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'C' and resid 471 through 476 removed outlier: 5.733A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 471 through 476 removed outlier: 5.733A pdb=" N ALA C 473 " --> pdb=" O GLY C 729 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLY C 729 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU C 475 " --> pdb=" O GLY C 727 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY C 727 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET C 492 " --> pdb=" O TYR C 728 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 642 through 644 removed outlier: 6.783A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 441 through 442 removed outlier: 3.516A pdb=" N VAL D 397 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 474 " --> pdb=" O VAL D 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB1, first strand: chain 'D' and resid 489 through 498 removed outlier: 5.378A pdb=" N ILE D 734 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR D 732 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET D 496 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LYS D 730 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.540A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 441 through 442 removed outlier: 3.519A pdb=" N VAL B 397 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 474 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 498 removed outlier: 5.375A pdb=" N ILE B 734 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR B 732 " --> pdb=" O PRO B 494 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET B 496 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LYS B 730 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.542A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 391 through 392 removed outlier: 6.405A pdb=" N TYR A 391 " --> pdb=" O ARG A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AB9, first strand: chain 'A' and resid 471 through 476 removed outlier: 5.724A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 471 through 476 removed outlier: 5.724A pdb=" N ALA A 473 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLY A 729 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 475 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 727 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N MET A 492 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 642 through 644 removed outlier: 6.787A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AC4, first strand: chain 'J' and resid 88 through 90 852 hydrogen bonds defined for protein. 2514 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: 5.22 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2468 1.32 - 1.45: 4634 1.45 - 1.59: 9014 1.59 - 1.72: 12 1.72 - 1.86: 154 Bond restraints: 16282 Sorted by residual: bond pdb=" CAW ZK1 B 901 " pdb=" NAY ZK1 B 901 " ideal model delta sigma weight residual 1.388 1.505 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" CAW ZK1 D 901 " pdb=" NAY ZK1 D 901 " ideal model delta sigma weight residual 1.388 1.503 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" CAW ZK1 C 901 " pdb=" NAY ZK1 C 901 " ideal model delta sigma weight residual 1.388 1.499 -0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" CAW ZK1 A 901 " pdb=" NAY ZK1 A 901 " ideal model delta sigma weight residual 1.388 1.498 -0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" CAV ZK1 B 901 " pdb=" NAP ZK1 B 901 " ideal model delta sigma weight residual 1.381 1.485 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 16277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.78: 21816 5.78 - 11.56: 96 11.56 - 17.34: 10 17.34 - 23.12: 16 23.12 - 28.90: 6 Bond angle restraints: 21944 Sorted by residual: angle pdb=" C35 POV A 905 " pdb=" C36 POV A 905 " pdb=" C37 POV A 905 " ideal model delta sigma weight residual 113.93 142.83 -28.90 3.00e+00 1.11e-01 9.28e+01 angle pdb=" C35 POV C 905 " pdb=" C36 POV C 905 " pdb=" C37 POV C 905 " ideal model delta sigma weight residual 113.93 142.82 -28.89 3.00e+00 1.11e-01 9.27e+01 angle pdb=" C35 POV A 902 " pdb=" C36 POV A 902 " pdb=" C37 POV A 902 " ideal model delta sigma weight residual 113.93 142.04 -28.11 3.00e+00 1.11e-01 8.78e+01 angle pdb=" C35 POV C 902 " pdb=" C36 POV C 902 " pdb=" C37 POV C 902 " ideal model delta sigma weight residual 113.93 142.00 -28.07 3.00e+00 1.11e-01 8.76e+01 angle pdb=" C35 POV D 905 " pdb=" C36 POV D 905 " pdb=" C37 POV D 905 " ideal model delta sigma weight residual 113.93 141.82 -27.89 3.00e+00 1.11e-01 8.64e+01 ... (remaining 21939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 9048 26.04 - 52.07: 502 52.07 - 78.11: 99 78.11 - 104.15: 27 104.15 - 130.18: 6 Dihedral angle restraints: 9682 sinusoidal: 3936 harmonic: 5746 Sorted by residual: dihedral pdb=" C27 POV B 905 " pdb=" C28 POV B 905 " pdb=" C29 POV B 905 " pdb="C210 POV B 905 " ideal model delta sinusoidal sigma weight residual 127.48 -102.34 -130.18 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C27 POV D 905 " pdb=" C28 POV D 905 " pdb=" C29 POV D 905 " pdb="C210 POV D 905 " ideal model delta sinusoidal sigma weight residual 127.48 -102.37 -130.15 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" CA SER D 497 " pdb=" C SER D 497 " pdb=" N LEU D 498 " pdb=" CA LEU D 498 " ideal model delta harmonic sigma weight residual 180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 9679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1761 0.044 - 0.088: 529 0.088 - 0.132: 108 0.132 - 0.176: 12 0.176 - 0.221: 6 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CB VAL C 600 " pdb=" CA VAL C 600 " pdb=" CG1 VAL C 600 " pdb=" CG2 VAL C 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL A 600 " pdb=" CA VAL A 600 " pdb=" CG1 VAL A 600 " pdb=" CG2 VAL A 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C22 OLC D 902 " pdb=" C21 OLC D 902 " pdb=" C24 OLC D 902 " pdb=" O23 OLC D 902 " both_signs ideal model delta sigma weight residual False -2.31 -2.50 0.19 2.00e-01 2.50e+01 9.10e-01 ... (remaining 2413 not shown) Planarity restraints: 2658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 744 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO B 745 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 744 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO D 745 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 745 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 745 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 519 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 520 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 520 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 520 " 0.025 5.00e-02 4.00e+02 ... (remaining 2655 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 200 2.64 - 3.20: 14771 3.20 - 3.77: 23344 3.77 - 4.33: 33442 4.33 - 4.90: 56074 Nonbonded interactions: 127831 Sorted by model distance: nonbonded pdb=" O ILE J 37 " pdb=" OG1 THR J 41 " model vdw 2.075 3.040 nonbonded pdb=" O ILE I 37 " pdb=" OG1 THR I 41 " model vdw 2.075 3.040 nonbonded pdb=" O VAL C 677 " pdb=" OH TYR C 696 " model vdw 2.209 3.040 nonbonded pdb=" O VAL A 677 " pdb=" OH TYR A 696 " model vdw 2.209 3.040 nonbonded pdb=" N ALA A 448 " pdb=" OD1 ASN A 457 " model vdw 2.231 3.120 ... (remaining 127826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 31 or resid 433 or resid 436 or (resid 438 and (name N or name CA or name C or n \ ame O or name CB )) or resid 440 through 441 or resid 443 through 450 or resid 4 \ 52 through 454 or resid 456 through 466 or resid 468 through 469 or resid 471 or \ resid 473 through 544 or (resid 545 through 546 and (name N or name CA or name \ C or name O or name CB )) or resid 567 through 581 or resid 583 through 635 or r \ esid 637 through 638 or (resid 639 through 640 and (name N or name CA or name C \ or name O or name CB )) or resid 641 through 646 or resid 649 through 663 or res \ id 665 through 670 or resid 672 through 679 or (resid 680 and (name N or name CA \ or name C or name O or name CB )) or resid 681 through 682 or resid 684 through \ 685 or resid 688 through 736 or resid 738 or resid 741 through 759 or (resid 76 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 762 through \ 770 or resid 772 through 777 or resid 779 through 795 or resid 797 through 815 o \ r resid 901 or resid 903 through 904 or (resid 905 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213)))) selection = (chain 'B' and (resid 397 through 402 or resid 404 through 407 or resid 409 or ( \ resid 410 and (name N or name CA or name C or name O or name CB )) or resid 411 \ or resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or re \ sid 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or (r \ esid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 o \ r (resid 458 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 60 through 470 or resid 472 through 473 or resid 475 or resid 477 through 507 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 585 or resid 587 through 639 or resid 641 through 650 or r \ esid 653 through 656 or (resid 657 and (name N or name CA or name C or name O or \ name CB )) or resid 658 through 667 or resid 669 through 674 or resid 676 throu \ gh 686 or resid 688 through 689 or resid 692 through 696 or (resid 697 and (name \ N or name CA or name C or name O or name CB )) or resid 698 through 718 or (res \ id 719 and (name N or name CA or name C or name O or name CB )) or resid 720 thr \ ough 740 or resid 742 or resid 745 through 763 or resid 765 through 774 or (resi \ d 776 through 778 and (name N or name CA or name C or name O or name CB )) or re \ sid 779 or (resid 780 through 781 and (name N or name CA or name C or name O or \ name CB )) or (resid 783 and (name N or name CA or name C or name O or name CB ) \ ) or resid 784 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 or (resid 90 \ 3 and (name CA or name CB or name CD or name CE or name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name CC or \ name O1 or name O2 )) or resid 904 through 905)) selection = (chain 'C' and (resid 393 through 398 or resid 400 through 403 or resid 405 thro \ ugh 407 or resid 412 through 414 or resid 416 through 422 or resid 424 through 4 \ 31 or resid 433 or resid 436 or (resid 438 and (name N or name CA or name C or n \ ame O or name CB )) or resid 440 through 441 or resid 443 through 450 or resid 4 \ 52 through 454 or resid 456 through 466 or resid 468 through 469 or resid 471 or \ resid 473 through 544 or (resid 545 through 546 and (name N or name CA or name \ C or name O or name CB )) or resid 567 through 581 or resid 583 through 635 or r \ esid 637 through 638 or (resid 639 through 640 and (name N or name CA or name C \ or name O or name CB )) or resid 641 through 646 or resid 649 through 663 or res \ id 665 through 670 or resid 672 through 679 or (resid 680 and (name N or name CA \ or name C or name O or name CB )) or resid 681 through 682 or resid 684 through \ 685 or resid 688 through 736 or resid 738 or resid 741 through 759 or (resid 76 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 762 through \ 770 or resid 772 through 777 or resid 779 through 795 or resid 797 through 815 o \ r resid 901 or resid 903 through 904 or (resid 905 and (name N or name C1 or nam \ e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 or n \ ame O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211 \ or name C212 or name C213)))) selection = (chain 'D' and (resid 397 through 402 or resid 404 through 407 or resid 409 or ( \ resid 410 and (name N or name CA or name C or name O or name CB )) or resid 411 \ or resid 416 through 418 or resid 420 through 426 or resid 428 through 435 or re \ sid 437 or resid 440 or resid 442 or resid 444 through 445 or resid 447 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or (r \ esid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 o \ r (resid 458 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 60 through 470 or resid 472 through 473 or resid 475 or resid 477 through 507 or \ (resid 508 through 509 and (name N or name CA or name C or name O or name CB )) \ or resid 510 through 585 or resid 587 through 639 or resid 641 through 650 or r \ esid 653 through 656 or (resid 657 and (name N or name CA or name C or name O or \ name CB )) or resid 658 through 667 or resid 669 through 674 or resid 676 throu \ gh 686 or resid 688 through 689 or resid 692 through 696 or (resid 697 and (name \ N or name CA or name C or name O or name CB )) or resid 698 through 718 or (res \ id 719 and (name N or name CA or name C or name O or name CB )) or resid 720 thr \ ough 740 or resid 742 or resid 745 through 763 or resid 765 through 774 or (resi \ d 776 through 778 and (name N or name CA or name C or name O or name CB )) or re \ sid 779 or (resid 780 through 781 and (name N or name CA or name C or name O or \ name CB )) or (resid 783 and (name N or name CA or name C or name O or name CB ) \ ) or resid 784 through 799 or resid 801 through 817 or (resid 818 through 819 an \ d (name N or name CA or name C or name O or name CB )) or resid 901 or (resid 90 \ 3 and (name CA or name CB or name CD or name CE or name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name CC or \ name O1 or name O2 )) or resid 904 through 905)) } ncs_group { reference = (chain 'I' and resid 16 through 234) selection = (chain 'J' and resid 16 through 234) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 37.380 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 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 0.117 16282 Z= 0.533 Angle : 1.270 28.901 21944 Z= 0.508 Chirality : 0.043 0.221 2416 Planarity : 0.004 0.057 2658 Dihedral : 17.620 130.182 6002 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.18), residues: 1980 helix: 0.28 (0.16), residues: 1080 sheet: -2.66 (0.41), residues: 138 loop : -1.10 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 460 HIS 0.010 0.002 HIS A 548 PHE 0.024 0.002 PHE B 541 TYR 0.031 0.002 TYR B 816 ARG 0.024 0.001 ARG C 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 1.607 Fit side-chains REVERT: C 421 CYS cc_start: 0.8024 (m) cc_final: 0.7784 (m) REVERT: C 638 GLN cc_start: 0.8017 (pp30) cc_final: 0.7607 (pp30) REVERT: A 421 CYS cc_start: 0.8065 (m) cc_final: 0.7716 (m) REVERT: A 638 GLN cc_start: 0.7962 (pp30) cc_final: 0.7549 (pp30) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.3154 time to fit residues: 123.3364 Evaluate side-chains 180 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS D 726 ASN B 726 ASN A 431 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16282 Z= 0.212 Angle : 0.580 14.903 21944 Z= 0.289 Chirality : 0.041 0.215 2416 Planarity : 0.004 0.058 2658 Dihedral : 13.888 151.026 2702 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.66 % Allowed : 7.33 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1980 helix: 1.71 (0.16), residues: 1094 sheet: -2.25 (0.39), residues: 138 loop : -1.15 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 460 HIS 0.008 0.001 HIS A 548 PHE 0.020 0.002 PHE A 810 TYR 0.016 0.001 TYR B 673 ARG 0.004 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8075 (m) cc_final: 0.7605 (m) REVERT: C 436 TYR cc_start: 0.7925 (p90) cc_final: 0.7625 (p90) REVERT: C 638 GLN cc_start: 0.8324 (pp30) cc_final: 0.7864 (pp30) REVERT: D 434 LYS cc_start: 0.7484 (tmmt) cc_final: 0.7206 (ttmt) REVERT: D 523 TYR cc_start: 0.7430 (m-10) cc_final: 0.7193 (m-10) REVERT: B 434 LYS cc_start: 0.7479 (tmmt) cc_final: 0.7197 (ttmt) REVERT: B 523 TYR cc_start: 0.7409 (m-10) cc_final: 0.7173 (m-10) REVERT: B 629 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6556 (pmm) REVERT: A 421 CYS cc_start: 0.8075 (m) cc_final: 0.7611 (m) REVERT: A 436 TYR cc_start: 0.7883 (p90) cc_final: 0.7552 (p90) REVERT: A 638 GLN cc_start: 0.8313 (pp30) cc_final: 0.7868 (pp30) outliers start: 26 outliers final: 14 residues processed: 230 average time/residue: 0.2954 time to fit residues: 101.7304 Evaluate side-chains 176 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 149 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS C 710 GLN C 752 GLN D 726 ASN B 726 ASN A 431 HIS A 710 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16282 Z= 0.189 Angle : 0.508 12.555 21944 Z= 0.258 Chirality : 0.040 0.238 2416 Planarity : 0.004 0.058 2658 Dihedral : 13.116 144.906 2702 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.79 % Allowed : 9.82 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1980 helix: 2.13 (0.16), residues: 1088 sheet: -1.94 (0.45), residues: 126 loop : -0.97 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 766 HIS 0.007 0.001 HIS A 548 PHE 0.011 0.001 PHE A 810 TYR 0.011 0.001 TYR C 401 ARG 0.003 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8125 (m) cc_final: 0.7632 (m) REVERT: C 436 TYR cc_start: 0.8083 (p90) cc_final: 0.7619 (p90) REVERT: C 638 GLN cc_start: 0.8386 (pp30) cc_final: 0.7787 (pp30) REVERT: D 434 LYS cc_start: 0.7664 (tmmt) cc_final: 0.7420 (ttmt) REVERT: D 523 TYR cc_start: 0.7686 (m-10) cc_final: 0.7475 (m-10) REVERT: D 714 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.7038 (tp40) REVERT: B 434 LYS cc_start: 0.7647 (tmmt) cc_final: 0.7394 (ttmt) REVERT: B 523 TYR cc_start: 0.7741 (m-10) cc_final: 0.7483 (m-10) REVERT: A 421 CYS cc_start: 0.8120 (m) cc_final: 0.7614 (m) REVERT: A 436 TYR cc_start: 0.8050 (p90) cc_final: 0.7573 (p90) REVERT: A 638 GLN cc_start: 0.8408 (pp30) cc_final: 0.7836 (pp30) REVERT: J 122 ARG cc_start: 0.7207 (mmt90) cc_final: 0.6994 (mmm-85) outliers start: 28 outliers final: 20 residues processed: 214 average time/residue: 0.2659 time to fit residues: 86.9483 Evaluate side-chains 195 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 714 GLN Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 729 SER Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain J residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 171 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16282 Z= 0.236 Angle : 0.527 14.264 21944 Z= 0.268 Chirality : 0.041 0.254 2416 Planarity : 0.004 0.058 2658 Dihedral : 12.832 143.944 2702 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.61 % Allowed : 11.03 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 1980 helix: 2.09 (0.16), residues: 1090 sheet: -1.76 (0.40), residues: 158 loop : -1.06 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 766 HIS 0.007 0.001 HIS A 548 PHE 0.014 0.001 PHE C 491 TYR 0.018 0.002 TYR A 812 ARG 0.002 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 1.672 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8109 (m) cc_final: 0.7694 (m) REVERT: C 492 MET cc_start: 0.9207 (ttp) cc_final: 0.8950 (ttm) REVERT: C 501 LYS cc_start: 0.8177 (tmtt) cc_final: 0.7920 (tttm) REVERT: C 638 GLN cc_start: 0.8462 (pp30) cc_final: 0.7667 (pp30) REVERT: D 434 LYS cc_start: 0.7669 (tmmt) cc_final: 0.7435 (ttmt) REVERT: D 642 GLN cc_start: 0.7432 (pp30) cc_final: 0.7010 (pp30) REVERT: B 434 LYS cc_start: 0.7615 (tmmt) cc_final: 0.7391 (ttmt) REVERT: B 642 GLN cc_start: 0.7579 (pp30) cc_final: 0.7292 (pp30) REVERT: A 421 CYS cc_start: 0.8095 (m) cc_final: 0.7677 (m) REVERT: A 492 MET cc_start: 0.9198 (ttp) cc_final: 0.8941 (ttm) REVERT: A 638 GLN cc_start: 0.8469 (pp30) cc_final: 0.7678 (pp30) outliers start: 41 outliers final: 29 residues processed: 210 average time/residue: 0.3001 time to fit residues: 94.0719 Evaluate side-chains 196 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 150 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 171 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN D 764 ASN A 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16282 Z= 0.184 Angle : 0.481 12.667 21944 Z= 0.246 Chirality : 0.039 0.242 2416 Planarity : 0.004 0.057 2658 Dihedral : 12.274 138.428 2702 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.85 % Allowed : 13.14 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1980 helix: 2.24 (0.16), residues: 1090 sheet: -1.63 (0.39), residues: 168 loop : -1.00 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 766 HIS 0.006 0.001 HIS A 548 PHE 0.010 0.001 PHE B 495 TYR 0.017 0.001 TYR C 812 ARG 0.003 0.000 ARG J 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: C 403 MET cc_start: 0.6701 (mtm) cc_final: 0.6490 (mtm) REVERT: C 421 CYS cc_start: 0.8150 (m) cc_final: 0.7839 (m) REVERT: C 492 MET cc_start: 0.9190 (ttp) cc_final: 0.8927 (ttm) REVERT: C 501 LYS cc_start: 0.8161 (tmtt) cc_final: 0.7911 (tttm) REVERT: C 638 GLN cc_start: 0.8417 (pp30) cc_final: 0.7679 (pp30) REVERT: D 434 LYS cc_start: 0.7723 (tmmt) cc_final: 0.7474 (ttmt) REVERT: D 642 GLN cc_start: 0.7597 (pp30) cc_final: 0.7199 (pp30) REVERT: B 434 LYS cc_start: 0.7636 (tmmt) cc_final: 0.7398 (ttmt) REVERT: B 642 GLN cc_start: 0.7590 (pp30) cc_final: 0.7333 (pp30) REVERT: A 421 CYS cc_start: 0.8055 (m) cc_final: 0.7757 (m) REVERT: A 492 MET cc_start: 0.9178 (ttp) cc_final: 0.8918 (ttm) REVERT: A 638 GLN cc_start: 0.8426 (pp30) cc_final: 0.7691 (pp30) outliers start: 29 outliers final: 24 residues processed: 200 average time/residue: 0.2872 time to fit residues: 85.9088 Evaluate side-chains 188 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16282 Z= 0.200 Angle : 0.480 12.143 21944 Z= 0.247 Chirality : 0.039 0.240 2416 Planarity : 0.003 0.057 2658 Dihedral : 12.069 132.023 2702 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.42 % Allowed : 13.58 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1980 helix: 2.25 (0.16), residues: 1090 sheet: -1.49 (0.40), residues: 168 loop : -1.02 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 766 HIS 0.007 0.001 HIS A 548 PHE 0.010 0.001 PHE A 580 TYR 0.018 0.001 TYR C 812 ARG 0.002 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.894 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8087 (m) cc_final: 0.7789 (m) REVERT: C 492 MET cc_start: 0.9211 (ttp) cc_final: 0.8942 (ttm) REVERT: C 501 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7939 (tttm) REVERT: C 638 GLN cc_start: 0.8381 (pp30) cc_final: 0.7637 (pp30) REVERT: D 434 LYS cc_start: 0.7744 (tmmt) cc_final: 0.7500 (ttmt) REVERT: D 642 GLN cc_start: 0.7538 (pp30) cc_final: 0.7137 (pp30) REVERT: B 434 LYS cc_start: 0.7662 (tmmt) cc_final: 0.7435 (ttmt) REVERT: B 642 GLN cc_start: 0.7566 (pp30) cc_final: 0.7179 (pp30) REVERT: B 674 MET cc_start: 0.7314 (mmm) cc_final: 0.6984 (mmm) REVERT: A 399 ASP cc_start: 0.7196 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: A 421 CYS cc_start: 0.8085 (m) cc_final: 0.7786 (m) REVERT: A 492 MET cc_start: 0.9202 (ttp) cc_final: 0.8932 (ttm) REVERT: A 638 GLN cc_start: 0.8350 (pp30) cc_final: 0.7632 (pp30) REVERT: J 122 ARG cc_start: 0.7351 (mmt90) cc_final: 0.7006 (mmm-85) outliers start: 38 outliers final: 29 residues processed: 205 average time/residue: 0.2780 time to fit residues: 86.1532 Evaluate side-chains 190 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 190 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16282 Z= 0.161 Angle : 0.465 11.358 21944 Z= 0.237 Chirality : 0.039 0.230 2416 Planarity : 0.003 0.055 2658 Dihedral : 11.510 119.634 2702 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.72 % Allowed : 14.73 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1980 helix: 2.39 (0.16), residues: 1092 sheet: -1.42 (0.42), residues: 150 loop : -0.98 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 766 HIS 0.006 0.001 HIS A 548 PHE 0.014 0.001 PHE A 810 TYR 0.018 0.001 TYR A 812 ARG 0.002 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8172 (m) cc_final: 0.7875 (m) REVERT: C 492 MET cc_start: 0.9189 (ttp) cc_final: 0.8927 (ttm) REVERT: C 638 GLN cc_start: 0.8301 (pp30) cc_final: 0.7582 (pp30) REVERT: D 434 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7502 (ttmt) REVERT: B 434 LYS cc_start: 0.7678 (tmmt) cc_final: 0.7455 (ttmt) REVERT: B 642 GLN cc_start: 0.7586 (pp30) cc_final: 0.7314 (pp30) REVERT: B 674 MET cc_start: 0.7305 (mmm) cc_final: 0.6984 (mmm) REVERT: A 421 CYS cc_start: 0.8163 (m) cc_final: 0.7865 (m) REVERT: A 492 MET cc_start: 0.9179 (ttp) cc_final: 0.8917 (ttm) REVERT: A 638 GLN cc_start: 0.8315 (pp30) cc_final: 0.7610 (pp30) REVERT: J 122 ARG cc_start: 0.7430 (mmt90) cc_final: 0.7097 (mmm-85) outliers start: 27 outliers final: 24 residues processed: 193 average time/residue: 0.2891 time to fit residues: 83.8774 Evaluate side-chains 187 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 543 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16282 Z= 0.159 Angle : 0.469 11.220 21944 Z= 0.237 Chirality : 0.039 0.227 2416 Planarity : 0.003 0.056 2658 Dihedral : 11.248 101.959 2702 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.04 % Allowed : 14.29 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1980 helix: 2.42 (0.16), residues: 1096 sheet: -1.40 (0.42), residues: 150 loop : -0.93 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 766 HIS 0.007 0.001 HIS A 548 PHE 0.015 0.001 PHE C 810 TYR 0.019 0.001 TYR A 812 ARG 0.002 0.000 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.884 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8157 (m) cc_final: 0.7862 (m) REVERT: C 492 MET cc_start: 0.9187 (ttp) cc_final: 0.8925 (ttm) REVERT: B 434 LYS cc_start: 0.7683 (tmmt) cc_final: 0.7472 (ttmt) REVERT: B 642 GLN cc_start: 0.7574 (pp30) cc_final: 0.7312 (pp30) REVERT: B 674 MET cc_start: 0.7336 (mmm) cc_final: 0.7031 (mmm) REVERT: A 421 CYS cc_start: 0.8169 (m) cc_final: 0.7869 (m) REVERT: A 492 MET cc_start: 0.9180 (ttp) cc_final: 0.8917 (ttm) REVERT: J 122 ARG cc_start: 0.7460 (mmt90) cc_final: 0.7142 (mmm-85) outliers start: 32 outliers final: 22 residues processed: 179 average time/residue: 0.3122 time to fit residues: 85.1892 Evaluate side-chains 177 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 177 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16282 Z= 0.183 Angle : 0.484 10.905 21944 Z= 0.246 Chirality : 0.039 0.230 2416 Planarity : 0.003 0.056 2658 Dihedral : 11.212 87.378 2702 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.04 % Allowed : 14.29 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1980 helix: 2.42 (0.16), residues: 1094 sheet: -1.35 (0.44), residues: 140 loop : -0.94 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 766 HIS 0.007 0.001 HIS A 548 PHE 0.014 0.001 PHE A 810 TYR 0.020 0.001 TYR C 812 ARG 0.002 0.000 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8216 (m) cc_final: 0.7925 (m) REVERT: C 492 MET cc_start: 0.9195 (ttp) cc_final: 0.8933 (ttm) REVERT: B 434 LYS cc_start: 0.7695 (tmmt) cc_final: 0.7480 (ttmt) REVERT: B 642 GLN cc_start: 0.7592 (pp30) cc_final: 0.7299 (pp30) REVERT: B 674 MET cc_start: 0.7352 (mmm) cc_final: 0.7036 (mmm) REVERT: A 421 CYS cc_start: 0.8137 (m) cc_final: 0.7835 (m) REVERT: A 492 MET cc_start: 0.9187 (ttp) cc_final: 0.8921 (ttm) REVERT: J 122 ARG cc_start: 0.7465 (mmt90) cc_final: 0.7148 (mmm-85) outliers start: 32 outliers final: 28 residues processed: 180 average time/residue: 0.2927 time to fit residues: 78.7337 Evaluate side-chains 179 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 121 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 714 GLN J 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16282 Z= 0.169 Angle : 0.475 10.768 21944 Z= 0.241 Chirality : 0.039 0.224 2416 Planarity : 0.003 0.055 2658 Dihedral : 10.897 87.230 2702 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.72 % Allowed : 14.54 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1980 helix: 2.47 (0.16), residues: 1094 sheet: -1.32 (0.44), residues: 140 loop : -0.93 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 766 HIS 0.006 0.001 HIS A 548 PHE 0.013 0.001 PHE C 810 TYR 0.020 0.001 TYR A 812 ARG 0.002 0.000 ARG D 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8212 (m) cc_final: 0.7908 (m) REVERT: C 492 MET cc_start: 0.9190 (ttp) cc_final: 0.8927 (ttm) REVERT: B 434 LYS cc_start: 0.7707 (tmmt) cc_final: 0.7488 (ttmt) REVERT: B 642 GLN cc_start: 0.7602 (pp30) cc_final: 0.7367 (pp30) REVERT: B 674 MET cc_start: 0.7321 (mmm) cc_final: 0.7069 (mmm) REVERT: A 421 CYS cc_start: 0.8137 (m) cc_final: 0.7826 (m) REVERT: A 492 MET cc_start: 0.9195 (ttp) cc_final: 0.8939 (ttm) outliers start: 27 outliers final: 26 residues processed: 181 average time/residue: 0.3042 time to fit residues: 81.8567 Evaluate side-chains 186 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 496 ILE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 708 MET Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 708 MET Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 543 SER Chi-restraints excluded: chain A residue 623 GLU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 719 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.0020 chunk 157 optimal weight: 0.0370 chunk 65 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN J 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124740 restraints weight = 19946.528| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.82 r_work: 0.3084 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16282 Z= 0.160 Angle : 0.472 10.458 21944 Z= 0.240 Chirality : 0.039 0.218 2416 Planarity : 0.003 0.055 2658 Dihedral : 10.739 87.932 2702 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.66 % Allowed : 14.92 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.20), residues: 1980 helix: 2.48 (0.16), residues: 1094 sheet: -1.35 (0.44), residues: 140 loop : -0.94 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 766 HIS 0.006 0.001 HIS A 548 PHE 0.015 0.001 PHE A 810 TYR 0.020 0.001 TYR C 812 ARG 0.004 0.000 ARG A 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.63 seconds wall clock time: 56 minutes 55.44 seconds (3415.44 seconds total)