Starting phenix.real_space_refine on Fri Jul 3 22:19:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_15716.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_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_15716/07_2026/8aym_15716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_15716.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_15716.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_15716.cif" model { file = "/net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_15716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aym_15716/07_2026/8aym_15716.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} 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: {'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU: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: {'HIS:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'HIS:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU: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: {'GLU:plan': 4, 'ASP:plan': 3, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} 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: 3.15, per 1000 atoms: 0.20 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: 1.22 Conformation dependent library (CDL) restraints added in 763.6 milliseconds 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: 0.49 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: 2.37 Time building geometry restraints manager: 1.68 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: 8957 26.04 - 52.07: 487 52.07 - 78.11: 93 78.11 - 104.15: 27 104.15 - 130.18: 2 Dihedral angle restraints: 9566 sinusoidal: 3820 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 9563 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 901 o \ r resid 903 through 904 or (resid 905 and (name N or name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or n \ ame 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 C \ 36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 or na \ me 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 901 o \ r resid 903 through 904 or (resid 905 and (name N or name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or n \ ame 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 C \ 36 or name C37 or name O11 or name O12 or name O13 or name O14 or name O21 or na \ me 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: 1.940 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.080 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 16290 Z= 0.374 Angle : 1.271 28.901 21960 Z= 0.508 Chirality : 0.043 0.221 2416 Planarity : 0.004 0.057 2658 Dihedral : 17.302 130.182 5886 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (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 ARG 0.024 0.001 ARG C 624 TYR 0.031 0.002 TYR B 816 PHE 0.024 0.002 PHE B 541 TRP 0.023 0.002 TRP B 460 HIS 0.010 0.002 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.37 (16282) covalent geometry : angle 1.26995 / 0.51 (21944) SS BOND : bond 0.00258 / 0.16 ( 8) SS BOND : angle 1.94160 / 1.18 ( 16) hydrogen bonds : bond 0.21522 / 14.68 ( 848) hydrogen bonds : angle 7.55694 / 5.49 ( 2514) *********************** 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 : 0.516 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: 0.1301 time to fit residues: 51.1751 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 431 HIS D 726 ASN B 726 ASN A 431 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129546 restraints weight = 20089.504| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.90 r_work: 0.3140 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16290 Z= 0.149 Angle : 0.581 14.890 21960 Z= 0.291 Chirality : 0.041 0.195 2416 Planarity : 0.004 0.058 2658 Dihedral : 13.628 150.743 2586 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.66 % Allowed : 7.08 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1980 helix: 1.69 (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 ARG 0.003 0.000 ARG D 485 TYR 0.017 0.002 TYR B 673 PHE 0.020 0.002 PHE A 810 TRP 0.015 0.002 TRP D 460 HIS 0.008 0.002 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16282) covalent geometry : angle 0.58079 / 0.29 (21944) SS BOND : bond 0.00435 / 0.26 ( 8) SS BOND : angle 1.02166 / 0.71 ( 16) hydrogen bonds : bond 0.04487 / 3.04 ( 848) hydrogen bonds : angle 4.26551 / 3.08 ( 2514) *********************** 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 241 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8592 (m) cc_final: 0.7976 (m) REVERT: C 436 TYR cc_start: 0.8204 (p90) cc_final: 0.7882 (p90) REVERT: C 523 MET cc_start: 0.8737 (mmm) cc_final: 0.8463 (mmm) REVERT: C 638 GLN cc_start: 0.7986 (pp30) cc_final: 0.7407 (pp30) REVERT: C 748 LYS cc_start: 0.7859 (tttp) cc_final: 0.7607 (tttp) REVERT: D 434 LYS cc_start: 0.7255 (tmmt) cc_final: 0.6865 (ttmt) REVERT: D 523 TYR cc_start: 0.8130 (m-10) cc_final: 0.7880 (m-10) REVERT: B 434 LYS cc_start: 0.7217 (tmmt) cc_final: 0.6826 (ttmt) REVERT: B 523 TYR cc_start: 0.8101 (m-10) cc_final: 0.7845 (m-10) REVERT: B 629 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7115 (pmm) REVERT: A 421 CYS cc_start: 0.8587 (m) cc_final: 0.7967 (m) REVERT: A 436 TYR cc_start: 0.8180 (p90) cc_final: 0.7820 (p90) REVERT: A 638 GLN cc_start: 0.7987 (pp30) cc_final: 0.7428 (pp30) REVERT: A 678 PHE cc_start: 0.6923 (m-80) cc_final: 0.6580 (m-80) REVERT: A 748 LYS cc_start: 0.7839 (tttp) cc_final: 0.7598 (tttp) outliers start: 26 outliers final: 14 residues processed: 229 average time/residue: 0.1129 time to fit residues: 38.6846 Evaluate side-chains 181 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 156 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 0.5980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 431 HIS C 710 GLN D 726 ASN B 726 ASN A 431 HIS A 710 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125093 restraints weight = 20572.929| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.30 r_work: 0.3037 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16290 Z= 0.141 Angle : 0.513 12.892 21960 Z= 0.264 Chirality : 0.040 0.233 2416 Planarity : 0.004 0.058 2658 Dihedral : 12.979 149.931 2586 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.66 % Allowed : 10.01 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1980 helix: 2.05 (0.16), residues: 1090 sheet: -1.94 (0.45), residues: 126 loop : -0.99 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 485 TYR 0.011 0.001 TYR C 401 PHE 0.013 0.001 PHE A 678 TRP 0.027 0.002 TRP D 460 HIS 0.007 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (16282) covalent geometry : angle 0.51243 / 0.26 (21944) SS BOND : bond 0.00293 / 0.18 ( 8) SS BOND : angle 0.84386 / 0.56 ( 16) hydrogen bonds : bond 0.04437 / 3.04 ( 848) hydrogen bonds : angle 4.07431 / 2.94 ( 2514) *********************** 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 228 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8772 (m) cc_final: 0.8173 (m) REVERT: C 436 TYR cc_start: 0.8413 (p90) cc_final: 0.7851 (p90) REVERT: C 586 ASP cc_start: 0.7921 (p0) cc_final: 0.7356 (t70) REVERT: C 638 GLN cc_start: 0.8042 (pp30) cc_final: 0.7294 (pp30) REVERT: D 407 MET cc_start: 0.4995 (mtm) cc_final: 0.4562 (mtm) REVERT: D 434 LYS cc_start: 0.7552 (tmmt) cc_final: 0.7183 (ttmt) REVERT: D 523 TYR cc_start: 0.8544 (m-10) cc_final: 0.8267 (m-10) REVERT: D 629 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7286 (pmm) REVERT: D 714 GLN cc_start: 0.7774 (tp40) cc_final: 0.7556 (tp40) REVERT: D 816 TYR cc_start: 0.6671 (t80) cc_final: 0.6352 (t80) REVERT: B 434 LYS cc_start: 0.7516 (tmmt) cc_final: 0.7146 (ttmt) REVERT: B 523 TYR cc_start: 0.8550 (m-10) cc_final: 0.8277 (m-10) REVERT: B 629 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7266 (pmm) REVERT: B 714 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7472 (tp40) REVERT: B 766 TRP cc_start: 0.6933 (m100) cc_final: 0.6716 (m100) REVERT: B 816 TYR cc_start: 0.6667 (t80) cc_final: 0.6338 (t80) REVERT: A 421 CYS cc_start: 0.8774 (m) cc_final: 0.8175 (m) REVERT: A 436 TYR cc_start: 0.8378 (p90) cc_final: 0.7813 (p90) REVERT: A 523 MET cc_start: 0.8909 (mmm) cc_final: 0.8706 (mmm) REVERT: A 638 GLN cc_start: 0.8008 (pp30) cc_final: 0.7297 (pp30) outliers start: 26 outliers final: 20 residues processed: 219 average time/residue: 0.1110 time to fit residues: 37.4093 Evaluate side-chains 198 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 719 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 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 629 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 714 GLN Chi-restraints excluded: chain B residue 755 GLU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 VAL 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 101 optimal weight: 0.4980 chunk 93 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 710 GLN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126271 restraints weight = 20071.964| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.95 r_work: 0.3065 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16290 Z= 0.125 Angle : 0.474 12.700 21960 Z= 0.246 Chirality : 0.039 0.242 2416 Planarity : 0.004 0.057 2658 Dihedral : 12.297 146.107 2586 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.23 % Allowed : 11.35 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 1980 helix: 2.21 (0.16), residues: 1090 sheet: -1.70 (0.43), residues: 140 loop : -1.02 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 88 TYR 0.017 0.001 TYR A 812 PHE 0.010 0.001 PHE D 495 TRP 0.009 0.001 TRP B 766 HIS 0.007 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (16282) covalent geometry : angle 0.47332 / 0.25 (21944) SS BOND : bond 0.00269 / 0.16 ( 8) SS BOND : angle 0.91397 / 0.60 ( 16) hydrogen bonds : bond 0.03945 / 2.70 ( 848) hydrogen bonds : angle 3.93148 / 2.83 ( 2514) *********************** 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 213 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: C 391 TYR cc_start: 0.7876 (m-80) cc_final: 0.7559 (m-80) REVERT: C 421 CYS cc_start: 0.8763 (m) cc_final: 0.8139 (m) REVERT: C 436 TYR cc_start: 0.8516 (p90) cc_final: 0.7898 (p90) REVERT: C 492 MET cc_start: 0.9339 (ttp) cc_final: 0.9097 (ttm) REVERT: C 501 LYS cc_start: 0.8265 (tmtt) cc_final: 0.7918 (tttm) REVERT: C 638 GLN cc_start: 0.8058 (pp30) cc_final: 0.7204 (pp30) REVERT: D 407 MET cc_start: 0.4843 (mtm) cc_final: 0.4460 (mtm) REVERT: D 434 LYS cc_start: 0.7554 (tmmt) cc_final: 0.7189 (ttmt) REVERT: D 523 TYR cc_start: 0.8477 (m-10) cc_final: 0.8272 (m-10) REVERT: D 629 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7339 (pmm) REVERT: D 642 GLN cc_start: 0.7435 (pp30) cc_final: 0.6821 (pp30) REVERT: D 813 GLU cc_start: 0.7776 (tt0) cc_final: 0.7291 (mm-30) REVERT: D 816 TYR cc_start: 0.6874 (t80) cc_final: 0.6509 (t80) REVERT: B 434 LYS cc_start: 0.7536 (tmmt) cc_final: 0.7173 (ttmt) REVERT: B 460 TRP cc_start: 0.6902 (m100) cc_final: 0.6584 (m100) REVERT: B 629 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7329 (pmm) REVERT: B 642 GLN cc_start: 0.7405 (pp30) cc_final: 0.7094 (pp30) REVERT: B 714 GLN cc_start: 0.7749 (tp40) cc_final: 0.7400 (tp40) REVERT: B 813 GLU cc_start: 0.7779 (tt0) cc_final: 0.7295 (mm-30) REVERT: B 816 TYR cc_start: 0.6875 (t80) cc_final: 0.6512 (t80) REVERT: A 391 TYR cc_start: 0.7924 (m-80) cc_final: 0.7633 (m-80) REVERT: A 421 CYS cc_start: 0.8726 (m) cc_final: 0.8129 (m) REVERT: A 492 MET cc_start: 0.9339 (ttp) cc_final: 0.9097 (ttm) REVERT: A 501 LYS cc_start: 0.8328 (tmtt) cc_final: 0.8085 (tttm) REVERT: A 638 GLN cc_start: 0.8018 (pp30) cc_final: 0.7177 (pp30) REVERT: J 154 LYS cc_start: 0.7336 (mptt) cc_final: 0.7124 (mmmm) outliers start: 35 outliers final: 26 residues processed: 202 average time/residue: 0.1124 time to fit residues: 34.1893 Evaluate side-chains 200 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 591 ILE Chi-restraints excluded: chain D residue 629 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 591 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 635 SER 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 Chi-restraints excluded: chain A residue 807 LEU 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 173 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 3 optimal weight: 0.0010 chunk 112 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 710 GLN A 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.161335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125942 restraints weight = 20092.866| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.88 r_work: 0.3085 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16290 Z= 0.116 Angle : 0.459 12.346 21960 Z= 0.238 Chirality : 0.039 0.235 2416 Planarity : 0.004 0.057 2658 Dihedral : 11.806 137.602 2586 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.91 % Allowed : 12.63 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1980 helix: 2.30 (0.16), residues: 1090 sheet: -1.58 (0.42), residues: 150 loop : -0.96 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 739 TYR 0.016 0.001 TYR C 812 PHE 0.010 0.001 PHE A 580 TRP 0.008 0.001 TRP J 203 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16282) covalent geometry : angle 0.45806 / 0.24 (21944) SS BOND : bond 0.00164 / 0.10 ( 8) SS BOND : angle 0.92463 / 0.58 ( 16) hydrogen bonds : bond 0.03863 / 2.65 ( 848) hydrogen bonds : angle 3.90311 / 2.80 ( 2514) *********************** 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 223 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: C 391 TYR cc_start: 0.7934 (m-80) cc_final: 0.7606 (m-80) REVERT: C 403 MET cc_start: 0.7063 (mtm) cc_final: 0.6850 (mtm) REVERT: C 421 CYS cc_start: 0.8739 (m) cc_final: 0.8391 (m) REVERT: C 492 MET cc_start: 0.9345 (ttp) cc_final: 0.9091 (ttm) REVERT: C 501 LYS cc_start: 0.8225 (tmtt) cc_final: 0.7882 (tttm) REVERT: C 638 GLN cc_start: 0.8030 (pp30) cc_final: 0.7224 (pp30) REVERT: D 407 MET cc_start: 0.5124 (mtm) cc_final: 0.4786 (mtm) REVERT: D 434 LYS cc_start: 0.7597 (tmmt) cc_final: 0.7215 (ttmt) REVERT: D 629 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7285 (pmm) REVERT: D 642 GLN cc_start: 0.7356 (pp30) cc_final: 0.6818 (pp30) REVERT: D 813 GLU cc_start: 0.7741 (tt0) cc_final: 0.7211 (mm-30) REVERT: D 816 TYR cc_start: 0.6650 (t80) cc_final: 0.6259 (t80) REVERT: B 434 LYS cc_start: 0.7527 (tmmt) cc_final: 0.7155 (ttmt) REVERT: B 460 TRP cc_start: 0.6858 (m100) cc_final: 0.6587 (m100) REVERT: B 629 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7271 (pmm) REVERT: B 642 GLN cc_start: 0.7431 (pp30) cc_final: 0.7101 (pp30) REVERT: B 714 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: B 813 GLU cc_start: 0.7746 (tt0) cc_final: 0.7206 (mm-30) REVERT: B 816 TYR cc_start: 0.6635 (t80) cc_final: 0.6273 (t80) REVERT: A 391 TYR cc_start: 0.7944 (m-80) cc_final: 0.7620 (m-80) REVERT: A 421 CYS cc_start: 0.8727 (m) cc_final: 0.8379 (m) REVERT: A 492 MET cc_start: 0.9334 (ttp) cc_final: 0.9082 (ttm) REVERT: A 501 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7976 (tptm) REVERT: A 638 GLN cc_start: 0.8011 (pp30) cc_final: 0.7218 (pp30) REVERT: J 154 LYS cc_start: 0.7340 (mptt) cc_final: 0.7086 (mmmm) outliers start: 30 outliers final: 23 residues processed: 211 average time/residue: 0.1201 time to fit residues: 37.6822 Evaluate side-chains 196 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 635 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 629 MET Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 714 GLN 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 27 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 710 GLN C 752 GLN A 710 GLN A 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.160134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124613 restraints weight = 20128.900| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.96 r_work: 0.3061 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16290 Z= 0.129 Angle : 0.461 11.907 21960 Z= 0.241 Chirality : 0.039 0.236 2416 Planarity : 0.003 0.057 2658 Dihedral : 11.741 131.612 2586 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.74 % Allowed : 13.33 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1980 helix: 2.31 (0.16), residues: 1090 sheet: -1.44 (0.43), residues: 150 loop : -0.99 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 739 TYR 0.018 0.001 TYR A 812 PHE 0.010 0.001 PHE A 580 TRP 0.007 0.001 TRP A 574 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (16282) covalent geometry : angle 0.46013 / 0.24 (21944) SS BOND : bond 0.00357 / 0.21 ( 8) SS BOND : angle 0.98498 / 0.61 ( 16) hydrogen bonds : bond 0.03961 / 2.71 ( 848) hydrogen bonds : angle 3.89591 / 2.80 ( 2514) *********************** 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 214 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: C 403 MET cc_start: 0.7137 (mtm) cc_final: 0.6929 (mtm) REVERT: C 421 CYS cc_start: 0.8802 (m) cc_final: 0.8455 (m) REVERT: C 439 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: C 492 MET cc_start: 0.9358 (ttp) cc_final: 0.9105 (ttm) REVERT: C 501 LYS cc_start: 0.8236 (tmtt) cc_final: 0.7932 (tttm) REVERT: C 638 GLN cc_start: 0.8034 (pp30) cc_final: 0.7239 (pp30) REVERT: C 807 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7565 (tp) REVERT: D 407 MET cc_start: 0.5033 (mtm) cc_final: 0.4685 (mtm) REVERT: D 434 LYS cc_start: 0.7624 (tmmt) cc_final: 0.7247 (ttmt) REVERT: D 629 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7304 (pmm) REVERT: D 813 GLU cc_start: 0.7774 (tt0) cc_final: 0.7219 (mm-30) REVERT: D 816 TYR cc_start: 0.6668 (t80) cc_final: 0.6265 (t80) REVERT: B 434 LYS cc_start: 0.7552 (tmmt) cc_final: 0.7181 (ttmt) REVERT: B 629 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7255 (pmm) REVERT: B 642 GLN cc_start: 0.7464 (pp30) cc_final: 0.7070 (pp30) REVERT: B 714 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7474 (tp40) REVERT: B 768 TYR cc_start: 0.7509 (m-10) cc_final: 0.7292 (m-10) REVERT: B 813 GLU cc_start: 0.7772 (tt0) cc_final: 0.7217 (mm-30) REVERT: B 816 TYR cc_start: 0.6736 (t80) cc_final: 0.6321 (t80) REVERT: A 391 TYR cc_start: 0.7937 (m-80) cc_final: 0.7633 (m-80) REVERT: A 421 CYS cc_start: 0.8803 (m) cc_final: 0.8451 (m) REVERT: A 492 MET cc_start: 0.9358 (ttp) cc_final: 0.9110 (ttm) REVERT: A 501 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7863 (tttm) REVERT: A 638 GLN cc_start: 0.8023 (pp30) cc_final: 0.7242 (pp30) REVERT: J 154 LYS cc_start: 0.7364 (mptt) cc_final: 0.7088 (mmmm) outliers start: 43 outliers final: 28 residues processed: 201 average time/residue: 0.1171 time to fit residues: 35.3389 Evaluate side-chains 199 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 439 GLU 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 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 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 635 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 591 ILE Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 714 GLN 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 689 VAL 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 189 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 193 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.159556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124156 restraints weight = 20017.488| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.02 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16290 Z= 0.126 Angle : 0.465 11.965 21960 Z= 0.240 Chirality : 0.039 0.234 2416 Planarity : 0.003 0.056 2658 Dihedral : 11.441 120.039 2586 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.55 % Allowed : 13.39 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1980 helix: 2.35 (0.16), residues: 1092 sheet: -1.40 (0.42), residues: 150 loop : -0.96 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 624 TYR 0.019 0.001 TYR C 812 PHE 0.009 0.001 PHE C 580 TRP 0.008 0.001 TRP I 203 HIS 0.007 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16282) covalent geometry : angle 0.46432 / 0.24 (21944) SS BOND : bond 0.00326 / 0.19 ( 8) SS BOND : angle 1.06469 / 0.65 ( 16) hydrogen bonds : bond 0.03901 / 2.67 ( 848) hydrogen bonds : angle 3.87500 / 2.79 ( 2514) *********************** 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 219 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: C 391 TYR cc_start: 0.7929 (m-80) cc_final: 0.7718 (m-80) REVERT: C 421 CYS cc_start: 0.8783 (m) cc_final: 0.8423 (m) REVERT: C 492 MET cc_start: 0.9348 (ttp) cc_final: 0.9097 (ttm) REVERT: C 501 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7910 (tttm) REVERT: C 638 GLN cc_start: 0.7995 (pp30) cc_final: 0.7207 (pp30) REVERT: C 807 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7568 (tt) REVERT: D 407 MET cc_start: 0.5122 (mtm) cc_final: 0.4896 (mtm) REVERT: D 434 LYS cc_start: 0.7589 (tmmt) cc_final: 0.7232 (ttmt) REVERT: D 629 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7198 (pmm) REVERT: D 709 ASN cc_start: 0.8537 (t0) cc_final: 0.8086 (m-40) REVERT: D 813 GLU cc_start: 0.7843 (tt0) cc_final: 0.7332 (mm-30) REVERT: D 816 TYR cc_start: 0.6706 (t80) cc_final: 0.6246 (t80) REVERT: B 434 LYS cc_start: 0.7585 (tmmt) cc_final: 0.7223 (ttmt) REVERT: B 642 GLN cc_start: 0.7439 (pp30) cc_final: 0.7078 (pp30) REVERT: B 709 ASN cc_start: 0.8533 (t0) cc_final: 0.8085 (m-40) REVERT: B 714 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7509 (tp40) REVERT: B 813 GLU cc_start: 0.7828 (tt0) cc_final: 0.7334 (mm-30) REVERT: B 816 TYR cc_start: 0.6746 (t80) cc_final: 0.6291 (t80) REVERT: A 391 TYR cc_start: 0.7969 (m-80) cc_final: 0.7737 (m-80) REVERT: A 421 CYS cc_start: 0.8780 (m) cc_final: 0.8420 (m) REVERT: A 501 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7892 (tttm) REVERT: A 638 GLN cc_start: 0.7880 (pp30) cc_final: 0.7119 (pp30) REVERT: J 154 LYS cc_start: 0.7379 (mptt) cc_final: 0.7089 (mmmm) outliers start: 40 outliers final: 32 residues processed: 206 average time/residue: 0.1086 time to fit residues: 33.8512 Evaluate side-chains 199 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 101 VAL 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 689 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 463 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain D residue 635 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 496 MET Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 714 GLN 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 689 VAL 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 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.159570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.124467 restraints weight = 20053.427| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.81 r_work: 0.3066 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16290 Z= 0.116 Angle : 0.452 11.381 21960 Z= 0.236 Chirality : 0.039 0.227 2416 Planarity : 0.003 0.056 2658 Dihedral : 11.189 106.411 2586 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.49 % Allowed : 13.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1980 helix: 2.39 (0.16), residues: 1094 sheet: -1.46 (0.42), residues: 150 loop : -0.94 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 739 TYR 0.019 0.001 TYR A 812 PHE 0.009 0.001 PHE C 580 TRP 0.008 0.001 TRP J 203 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (16282) covalent geometry : angle 0.45077 / 0.24 (21944) SS BOND : bond 0.00303 / 0.18 ( 8) SS BOND : angle 1.20954 / 0.73 ( 16) hydrogen bonds : bond 0.03790 / 2.59 ( 848) hydrogen bonds : angle 3.82790 / 2.75 ( 2514) *********************** 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 209 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8808 (m) cc_final: 0.8469 (m) REVERT: C 501 LYS cc_start: 0.8191 (tmtt) cc_final: 0.7887 (tttm) REVERT: C 638 GLN cc_start: 0.7976 (pp30) cc_final: 0.7182 (pp30) REVERT: D 434 LYS cc_start: 0.7585 (tmmt) cc_final: 0.7233 (ttmt) REVERT: D 709 ASN cc_start: 0.8527 (t0) cc_final: 0.8064 (m-40) REVERT: D 813 GLU cc_start: 0.7863 (tt0) cc_final: 0.7339 (mm-30) REVERT: D 816 TYR cc_start: 0.6738 (t80) cc_final: 0.6322 (t80) REVERT: B 434 LYS cc_start: 0.7590 (tmmt) cc_final: 0.7230 (ttmt) REVERT: B 642 GLN cc_start: 0.7466 (pp30) cc_final: 0.7052 (pp30) REVERT: B 709 ASN cc_start: 0.8580 (t0) cc_final: 0.8119 (m-40) REVERT: B 813 GLU cc_start: 0.7844 (tt0) cc_final: 0.7333 (mm-30) REVERT: B 816 TYR cc_start: 0.6755 (t80) cc_final: 0.6319 (t80) REVERT: A 421 CYS cc_start: 0.8780 (m) cc_final: 0.8421 (m) REVERT: A 501 LYS cc_start: 0.8230 (tmtt) cc_final: 0.7910 (tttm) REVERT: A 638 GLN cc_start: 0.7915 (pp30) cc_final: 0.7177 (pp30) REVERT: J 154 LYS cc_start: 0.7382 (mptt) cc_final: 0.7100 (mmmm) outliers start: 39 outliers final: 30 residues processed: 196 average time/residue: 0.1105 time to fit residues: 32.9477 Evaluate side-chains 195 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 689 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 463 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 591 ILE 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 496 MET Chi-restraints excluded: chain B residue 591 ILE 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 679 VAL Chi-restraints excluded: chain A residue 689 VAL 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 42 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 chunk 127 optimal weight: 0.8980 chunk 144 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.159757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123521 restraints weight = 20143.630| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.92 r_work: 0.3071 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16290 Z= 0.114 Angle : 0.455 10.785 21960 Z= 0.236 Chirality : 0.039 0.222 2416 Planarity : 0.003 0.056 2658 Dihedral : 11.045 86.329 2586 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.10 % Allowed : 14.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.20), residues: 1980 helix: 2.45 (0.16), residues: 1092 sheet: -1.47 (0.39), residues: 168 loop : -0.93 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 739 TYR 0.019 0.001 TYR A 812 PHE 0.014 0.001 PHE A 810 TRP 0.007 0.001 TRP J 203 HIS 0.007 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (16282) covalent geometry : angle 0.45371 / 0.24 (21944) SS BOND : bond 0.00250 / 0.15 ( 8) SS BOND : angle 1.26657 / 0.76 ( 16) hydrogen bonds : bond 0.03765 / 2.58 ( 848) hydrogen bonds : angle 3.81450 / 2.74 ( 2514) *********************** 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 202 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8798 (m) cc_final: 0.8451 (m) REVERT: C 501 LYS cc_start: 0.8205 (tmtt) cc_final: 0.7950 (tttm) REVERT: C 638 GLN cc_start: 0.7852 (pp30) cc_final: 0.7076 (pp30) REVERT: D 709 ASN cc_start: 0.8494 (t0) cc_final: 0.8064 (m-40) REVERT: D 813 GLU cc_start: 0.7810 (tt0) cc_final: 0.7298 (mm-30) REVERT: D 816 TYR cc_start: 0.6801 (t80) cc_final: 0.6351 (t80) REVERT: B 642 GLN cc_start: 0.7435 (pp30) cc_final: 0.7088 (pp30) REVERT: B 709 ASN cc_start: 0.8553 (t0) cc_final: 0.8111 (m-40) REVERT: B 813 GLU cc_start: 0.7803 (tt0) cc_final: 0.7292 (mm-30) REVERT: B 816 TYR cc_start: 0.6819 (t80) cc_final: 0.6369 (t80) REVERT: A 421 CYS cc_start: 0.8834 (m) cc_final: 0.8477 (m) REVERT: A 492 MET cc_start: 0.9365 (ttp) cc_final: 0.9160 (ttm) REVERT: A 501 LYS cc_start: 0.8184 (tmtt) cc_final: 0.7866 (tttm) REVERT: A 717 MET cc_start: 0.8718 (ptm) cc_final: 0.8367 (ptt) outliers start: 33 outliers final: 29 residues processed: 191 average time/residue: 0.1318 time to fit residues: 37.9477 Evaluate side-chains 193 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 591 ILE Chi-restraints excluded: chain D residue 633 ILE 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 496 MET Chi-restraints excluded: chain B residue 591 ILE 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 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 121 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124031 restraints weight = 20220.652| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.85 r_work: 0.3057 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16290 Z= 0.126 Angle : 0.466 12.040 21960 Z= 0.241 Chirality : 0.039 0.220 2416 Planarity : 0.003 0.056 2658 Dihedral : 11.020 87.511 2586 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.17 % Allowed : 14.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.20), residues: 1980 helix: 2.40 (0.16), residues: 1094 sheet: -1.41 (0.43), residues: 140 loop : -0.94 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 739 TYR 0.020 0.001 TYR A 812 PHE 0.010 0.001 PHE C 580 TRP 0.007 0.001 TRP A 574 HIS 0.007 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16282) covalent geometry : angle 0.46420 / 0.24 (21944) SS BOND : bond 0.00306 / 0.18 ( 8) SS BOND : angle 1.40242 / 0.84 ( 16) hydrogen bonds : bond 0.03902 / 2.67 ( 848) hydrogen bonds : angle 3.84165 / 2.76 ( 2514) ********************** 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 201 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: C 421 CYS cc_start: 0.8778 (m) cc_final: 0.8430 (m) REVERT: C 501 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7965 (tttm) REVERT: D 709 ASN cc_start: 0.8519 (t0) cc_final: 0.8066 (m-40) REVERT: D 813 GLU cc_start: 0.7817 (tt0) cc_final: 0.7248 (mm-30) REVERT: D 816 TYR cc_start: 0.6867 (t80) cc_final: 0.6385 (t80) REVERT: B 642 GLN cc_start: 0.7417 (pp30) cc_final: 0.7009 (pp30) REVERT: B 709 ASN cc_start: 0.8512 (t0) cc_final: 0.8045 (m-40) REVERT: B 813 GLU cc_start: 0.7788 (tt0) cc_final: 0.7240 (mm-30) REVERT: B 816 TYR cc_start: 0.6845 (t80) cc_final: 0.6388 (t80) REVERT: A 421 CYS cc_start: 0.8832 (m) cc_final: 0.8504 (m) REVERT: A 492 MET cc_start: 0.9381 (ttp) cc_final: 0.9176 (ttm) REVERT: A 501 LYS cc_start: 0.8207 (tmtt) cc_final: 0.7902 (tttm) outliers start: 34 outliers final: 30 residues processed: 193 average time/residue: 0.1384 time to fit residues: 39.8797 Evaluate side-chains 191 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 ILE 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 496 MET Chi-restraints excluded: chain B residue 591 ILE 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 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 50 optimal weight: 0.0050 chunk 158 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 101 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.3932 r_free = 0.3932 target = 0.162169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.122494 restraints weight = 20247.296| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.28 r_work: 0.3043 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16290 Z= 0.110 Angle : 0.453 11.331 21960 Z= 0.235 Chirality : 0.039 0.208 2416 Planarity : 0.003 0.056 2658 Dihedral : 10.807 86.916 2586 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.91 % Allowed : 14.86 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 1980 helix: 2.47 (0.16), residues: 1094 sheet: -1.40 (0.43), residues: 140 loop : -0.91 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 711 TYR 0.020 0.001 TYR A 812 PHE 0.014 0.001 PHE A 810 TRP 0.008 0.001 TRP J 203 HIS 0.006 0.001 HIS A 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (16282) covalent geometry : angle 0.45123 / 0.23 (21944) SS BOND : bond 0.00277 / 0.17 ( 8) SS BOND : angle 1.36797 / 0.82 ( 16) hydrogen bonds : bond 0.03680 / 2.52 ( 848) hydrogen bonds : angle 3.78981 / 2.71 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3156.11 seconds wall clock time: 54 minutes 52.69 seconds (3292.69 seconds total)