Starting phenix.real_space_refine on Mon May 19 13:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p3q_17392/05_2025/8p3q_17392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p3q_17392/05_2025/8p3q_17392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p3q_17392/05_2025/8p3q_17392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p3q_17392/05_2025/8p3q_17392.map" model { file = "/net/cci-nas-00/data/ceres_data/8p3q_17392/05_2025/8p3q_17392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p3q_17392/05_2025/8p3q_17392.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 125 5.16 5 C 11851 2.51 5 N 2840 2.21 5 O 3226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18047 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3059 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3037 Classifications: {'peptide': 398} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 385} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3025 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 13} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1364 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1373 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1369 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.68, per 1000 atoms: 0.59 Number of scatterers: 18047 At special positions: 0 Unit cell: (121.422, 119.977, 135.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 125 16.00 P 5 15.00 O 3226 8.00 N 2840 7.00 C 11851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.02 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.72 Conformation dependent library (CDL) restraints added in 2.2 seconds 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4166 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 27 sheets defined 61.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.741A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 575 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.526A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.752A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.702A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 removed outlier: 3.564A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 822 removed outlier: 3.664A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.738A pdb=" N TRP C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 624 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.927A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 705 through 714 removed outlier: 3.562A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.733A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.611A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 545 removed outlier: 3.512A pdb=" N TRP D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.646A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.566A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 823 removed outlier: 3.719A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 133 through 161 removed outlier: 3.727A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 210 removed outlier: 3.705A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 104 Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.102A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 160 Processing helix chain 'F' and resid 177 through 209 Processing helix chain 'G' and resid 7 through 30 Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.745A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 161 Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 30 removed outlier: 3.521A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 105 through 124 Processing helix chain 'H' and resid 132 through 161 removed outlier: 4.137A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 210 removed outlier: 3.861A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 480 through 481 removed outlier: 4.234A pdb=" N GLY A 731 " --> pdb=" O ILE A 481 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 505 removed outlier: 3.725A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 646 through 648 removed outlier: 5.745A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 394 through 399 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB1, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 5.994A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 394 through 399 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 489 through 498 removed outlier: 4.836A pdb=" N ILE C 734 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 732 " --> pdb=" O PRO C 494 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET C 496 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 730 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 502 through 505 Processing sheet with id=AB7, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.340A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 498 removed outlier: 6.969A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 5.669A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 702 " --> pdb=" O MET D 503 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 503 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AC4, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AC6, first strand: chain 'G' and resid 57 through 61 Processing sheet with id=AC7, first strand: chain 'G' and resid 65 through 67 Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 59 Processing sheet with id=AC9, first strand: chain 'H' and resid 65 through 66 1122 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 5.48 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: 2800 1.32 - 1.45: 5145 1.45 - 1.58: 10263 1.58 - 1.71: 10 1.71 - 1.84: 202 Bond restraints: 18420 Sorted by residual: bond pdb=" C VAL B 484 " pdb=" N ARG B 485 " ideal model delta sigma weight residual 1.334 1.410 -0.075 1.33e-02 5.65e+03 3.22e+01 bond pdb=" C ALA C 691 " pdb=" N ARG C 692 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.31e-02 5.83e+03 1.90e+01 bond pdb=" CA SER C 537 " pdb=" CB SER C 537 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.56e-02 4.11e+03 1.74e+01 bond pdb=" C LEU A 742 " pdb=" N ARG A 743 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" CA SER D 537 " pdb=" CB SER D 537 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.63e+01 ... (remaining 18415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 21357 1.92 - 3.84: 3114 3.84 - 5.76: 287 5.76 - 7.68: 44 7.68 - 9.60: 7 Bond angle restraints: 24809 Sorted by residual: angle pdb=" O VAL B 484 " pdb=" C VAL B 484 " pdb=" N ARG B 485 " ideal model delta sigma weight residual 121.87 131.47 -9.60 1.01e+00 9.80e-01 9.04e+01 angle pdb=" CA ALA B 477 " pdb=" C ALA B 477 " pdb=" N PRO B 478 " ideal model delta sigma weight residual 117.68 122.31 -4.63 7.10e-01 1.98e+00 4.26e+01 angle pdb=" O MET D 674 " pdb=" C MET D 674 " pdb=" N ARG D 675 " ideal model delta sigma weight residual 122.12 128.81 -6.69 1.06e+00 8.90e-01 3.99e+01 angle pdb=" O ALA D 452 " pdb=" C ALA D 452 " pdb=" N ARG D 453 " ideal model delta sigma weight residual 123.41 116.30 7.11 1.17e+00 7.31e-01 3.70e+01 angle pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" O GLU D 678 " ideal model delta sigma weight residual 119.99 114.87 5.12 8.70e-01 1.32e+00 3.46e+01 ... (remaining 24804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 10106 31.57 - 63.15: 621 63.15 - 94.72: 44 94.72 - 126.29: 5 126.29 - 157.87: 2 Dihedral angle restraints: 10778 sinusoidal: 4237 harmonic: 6541 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 4.92 88.08 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 12.31 80.69 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual -86.00 -13.66 -72.34 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 10775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1670 0.069 - 0.137: 891 0.137 - 0.206: 181 0.206 - 0.275: 19 0.275 - 0.344: 7 Chirality restraints: 2768 Sorted by residual: chirality pdb=" CB VAL B 543 " pdb=" CA VAL B 543 " pdb=" CG1 VAL B 543 " pdb=" CG2 VAL B 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CG LEU B 498 " pdb=" CB LEU B 498 " pdb=" CD1 LEU B 498 " pdb=" CD2 LEU B 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2765 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV G1103 " 0.026 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C29 POV G1103 " -0.064 2.00e-02 2.50e+03 pdb="C210 POV G1103 " 0.064 2.00e-02 2.50e+03 pdb="C211 POV G1103 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 541 " 0.028 2.00e-02 2.50e+03 3.15e-02 1.74e+01 pdb=" CG PHE B 541 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE B 541 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 541 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 PHE B 541 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 541 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 541 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 485 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG B 485 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG B 485 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 486 " -0.022 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6014 2.83 - 3.35: 18383 3.35 - 3.86: 32697 3.86 - 4.38: 38989 4.38 - 4.90: 61010 Nonbonded interactions: 157093 Sorted by model distance: nonbonded pdb=" O ARG A 453 " pdb=" C ASP A 454 " model vdw 2.310 3.270 nonbonded pdb=" O LEU E 63 " pdb=" NH2 ARG E 102 " model vdw 2.363 3.120 nonbonded pdb=" O ARG G 6 " pdb=" N VAL G 8 " model vdw 2.365 3.120 nonbonded pdb=" O SER E 104 " pdb=" OG SER E 104 " model vdw 2.433 3.040 nonbonded pdb=" O ARG E 131 " pdb=" N ASN E 133 " model vdw 2.438 3.120 ... (remaining 157088 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 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 625 or resid 635 through 812 o \ r (resid 813 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 14 through 818 or (resid 819 through 823 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'B' and (resid 393 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 551 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 593 or (resid \ 594 and (name N or name CA or name C or name O or name CB )) or resid 595 throug \ h 625 or resid 635 through 773 or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 625 or resid 635 through 812 or (resid 813 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 818 o \ r (resid 819 through 823 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'D' and (resid 393 through 551 or (resid 569 and (name N or name CA or na \ me C or name O or name CB )) or resid 570 through 593 or (resid 594 and (name N \ or name CA or name C or name O or name CB )) or resid 595 through 625 or resid 6 \ 35 through 773 or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 206 or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 206 or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 210)) } 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: 1.090 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.780 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.010 0.075 18432 Z= 0.620 Angle : 1.371 9.604 24833 Z= 0.948 Chirality : 0.080 0.344 2768 Planarity : 0.009 0.076 3018 Dihedral : 18.610 157.867 6576 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.86 % Favored : 93.15 % Rotamer: Outliers : 9.79 % Allowed : 8.42 % Favored : 81.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2235 helix: 0.03 (0.14), residues: 1302 sheet: -2.14 (0.38), residues: 126 loop : -2.49 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.007 TRP A 606 HIS 0.018 0.005 HIS D 435 PHE 0.061 0.007 PHE B 541 TYR 0.038 0.006 TYR D 549 ARG 0.041 0.004 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.16564 ( 1122) hydrogen bonds : angle 6.51900 ( 3240) SS BOND : bond 0.01071 ( 12) SS BOND : angle 2.77374 ( 24) covalent geometry : bond 0.00963 (18420) covalent geometry : angle 1.36914 (24809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 325 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: A 481 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8605 (OUTLIER) REVERT: A 503 MET cc_start: 0.7829 (ttm) cc_final: 0.7314 (ptm) REVERT: A 506 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8180 (ttmm) REVERT: A 713 GLU cc_start: 0.9325 (tt0) cc_final: 0.8923 (tp30) REVERT: A 721 MET cc_start: 0.9029 (ttt) cc_final: 0.8661 (tpp) REVERT: B 543 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8733 (m) REVERT: B 586 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.8873 (mmm160) REVERT: B 770 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3138 (mmmt) REVERT: C 407 MET cc_start: 0.2826 (OUTLIER) cc_final: 0.1439 (ptt) REVERT: C 408 MET cc_start: 0.1356 (mmm) cc_final: 0.0498 (pmm) REVERT: C 414 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.4498 (ptt) REVERT: C 633 ILE cc_start: 0.5540 (OUTLIER) cc_final: 0.5308 (mm) REVERT: C 647 TYR cc_start: 0.3256 (p90) cc_final: 0.2299 (p90) REVERT: C 666 VAL cc_start: 0.4182 (OUTLIER) cc_final: 0.3961 (p) REVERT: C 714 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7927 (mp10) REVERT: C 819 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8450 (ttt-90) REVERT: E 57 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9025 (p) REVERT: E 69 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (pt) REVERT: E 76 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9151 (mm) REVERT: E 95 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8931 (tp30) REVERT: F 9 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8951 (mt0) REVERT: F 10 MET cc_start: 0.9339 (tpp) cc_final: 0.8998 (mmm) REVERT: F 24 MET cc_start: 0.8564 (tpt) cc_final: 0.7937 (tpp) REVERT: F 69 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8931 (pt) REVERT: F 81 ASP cc_start: 0.9109 (t0) cc_final: 0.8649 (t0) REVERT: F 95 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: F 99 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8646 (mtm180) REVERT: G 37 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8143 (mmm-85) REVERT: G 41 LYS cc_start: 0.8533 (tptp) cc_final: 0.8130 (pptt) REVERT: G 131 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8490 (mmm160) REVERT: G 207 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9132 (pt0) REVERT: H 5 ASP cc_start: 0.6294 (m-30) cc_final: 0.5906 (m-30) REVERT: H 9 GLN cc_start: 0.8586 (mt0) cc_final: 0.8324 (mp-120) REVERT: H 41 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8279 (tptp) REVERT: H 78 LYS cc_start: 0.9146 (ptmt) cc_final: 0.8436 (pttm) REVERT: H 81 ASP cc_start: 0.9296 (t70) cc_final: 0.9060 (t70) REVERT: H 207 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8519 (mm110) outliers start: 178 outliers final: 41 residues processed: 468 average time/residue: 1.3530 time to fit residues: 702.3047 Evaluate side-chains 248 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 819 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 692 ARG Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 0.0270 chunk 175 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 619 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 587 GLN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 587 GLN D 619 ASN D 756 GLN E 160 ASN E 199 HIS F 60 HIS F 132 HIS F 160 ASN F 205 HIS G 160 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.160422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085426 restraints weight = 34976.636| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.46 r_work: 0.3089 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18432 Z= 0.151 Angle : 0.642 10.305 24833 Z= 0.336 Chirality : 0.042 0.190 2768 Planarity : 0.004 0.042 3018 Dihedral : 13.423 115.448 2932 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.18 % Favored : 96.55 % Rotamer: Outliers : 4.84 % Allowed : 18.21 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2235 helix: 1.77 (0.15), residues: 1324 sheet: -2.36 (0.38), residues: 113 loop : -1.80 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 766 HIS 0.005 0.001 HIS D 435 PHE 0.019 0.002 PHE H 127 TYR 0.017 0.002 TYR D 711 ARG 0.007 0.001 ARG B 594 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 1122) hydrogen bonds : angle 4.59580 ( 3240) SS BOND : bond 0.00546 ( 12) SS BOND : angle 1.46389 ( 24) covalent geometry : bond 0.00326 (18420) covalent geometry : angle 0.64104 (24809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8021 (mmm) cc_final: 0.7493 (mmt) REVERT: A 503 MET cc_start: 0.6586 (ttm) cc_final: 0.6308 (ptm) REVERT: A 545 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7629 (mmt180) REVERT: A 759 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5767 (mt) REVERT: B 586 ARG cc_start: 0.8945 (mmm-85) cc_final: 0.8294 (mmm160) REVERT: B 770 LYS cc_start: 0.4430 (OUTLIER) cc_final: 0.3829 (mmmt) REVERT: C 407 MET cc_start: 0.1139 (ptt) cc_final: 0.0759 (ptt) REVERT: C 408 MET cc_start: 0.1532 (mmm) cc_final: 0.0736 (mpt) REVERT: C 414 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.5907 (ptt) REVERT: C 463 MET cc_start: 0.2603 (mtm) cc_final: 0.1419 (ptp) REVERT: C 670 MET cc_start: 0.7481 (mtp) cc_final: 0.7210 (mpp) REVERT: C 674 MET cc_start: 0.4294 (mtt) cc_final: 0.3343 (mtp) REVERT: D 414 MET cc_start: 0.5134 (OUTLIER) cc_final: 0.4233 (pp-130) REVERT: D 659 PHE cc_start: 0.9142 (m-80) cc_final: 0.8845 (m-80) REVERT: D 703 LEU cc_start: 0.8478 (mt) cc_final: 0.8111 (tp) REVERT: D 705 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8466 (mm-30) REVERT: E 10 MET cc_start: 0.8643 (tpt) cc_final: 0.8401 (tpt) REVERT: E 37 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: E 57 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8817 (t) REVERT: E 69 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8271 (pt) REVERT: E 76 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8904 (mm) REVERT: E 95 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8481 (tp30) REVERT: E 102 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8479 (tpt90) REVERT: E 174 TYR cc_start: 0.8839 (p90) cc_final: 0.8572 (p90) REVERT: F 6 ARG cc_start: 0.8494 (tpt90) cc_final: 0.8099 (tpt90) REVERT: F 9 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8191 (mt0) REVERT: F 10 MET cc_start: 0.9127 (tpp) cc_final: 0.8908 (mmm) REVERT: F 24 MET cc_start: 0.8351 (tpt) cc_final: 0.7980 (tpp) REVERT: F 58 MET cc_start: 0.8784 (mmm) cc_final: 0.8524 (tpp) REVERT: F 69 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6858 (pt) REVERT: F 81 ASP cc_start: 0.8949 (t0) cc_final: 0.8462 (t0) REVERT: F 95 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: G 99 ARG cc_start: 0.9149 (mtt-85) cc_final: 0.8553 (ptp-110) REVERT: G 140 ILE cc_start: 0.9058 (mp) cc_final: 0.8791 (mp) REVERT: G 176 TYR cc_start: 0.9256 (m-80) cc_final: 0.8886 (m-80) REVERT: G 204 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: G 207 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8775 (pt0) REVERT: G 208 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8804 (mp) REVERT: H 5 ASP cc_start: 0.5382 (m-30) cc_final: 0.5032 (m-30) REVERT: H 9 GLN cc_start: 0.7598 (mt0) cc_final: 0.7121 (mp10) REVERT: H 78 LYS cc_start: 0.7760 (ptmt) cc_final: 0.6968 (pttm) REVERT: H 81 ASP cc_start: 0.8881 (t70) cc_final: 0.8565 (t0) outliers start: 88 outliers final: 23 residues processed: 311 average time/residue: 1.2142 time to fit residues: 425.3744 Evaluate side-chains 216 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 73 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 68 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 165 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN E 132 HIS G 133 ASN G 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.153945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078065 restraints weight = 35457.885| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.53 r_work: 0.2958 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 18432 Z= 0.398 Angle : 0.751 10.350 24833 Z= 0.393 Chirality : 0.047 0.208 2768 Planarity : 0.005 0.051 3018 Dihedral : 12.570 97.818 2845 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.65 % Favored : 95.08 % Rotamer: Outliers : 5.89 % Allowed : 19.25 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2235 helix: 1.68 (0.14), residues: 1333 sheet: -2.65 (0.34), residues: 138 loop : -1.72 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 766 HIS 0.008 0.002 HIS H 205 PHE 0.024 0.003 PHE E 107 TYR 0.021 0.002 TYR C 647 ARG 0.008 0.001 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.05505 ( 1122) hydrogen bonds : angle 4.81979 ( 3240) SS BOND : bond 0.00543 ( 12) SS BOND : angle 1.57161 ( 24) covalent geometry : bond 0.00923 (18420) covalent geometry : angle 0.74935 (24809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 171 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8260 (mmm) cc_final: 0.7784 (mmt) REVERT: A 503 MET cc_start: 0.6286 (ttm) cc_final: 0.5972 (ptm) REVERT: A 759 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5771 (mt) REVERT: B 586 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8400 (mmm160) REVERT: B 770 LYS cc_start: 0.4075 (OUTLIER) cc_final: 0.3625 (mmmt) REVERT: C 414 MET cc_start: 0.6921 (mtm) cc_final: 0.5994 (ptt) REVERT: C 647 TYR cc_start: 0.2715 (p90) cc_final: 0.2416 (p90) REVERT: D 414 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.4909 (pmm) REVERT: D 496 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.5113 (tmm) REVERT: D 659 PHE cc_start: 0.9128 (m-80) cc_final: 0.8802 (m-80) REVERT: D 732 TYR cc_start: 0.6515 (m-10) cc_final: 0.6257 (m-10) REVERT: E 5 ASP cc_start: 0.5723 (OUTLIER) cc_final: 0.5279 (p0) REVERT: E 32 TYR cc_start: 0.8873 (m-80) cc_final: 0.8663 (m-80) REVERT: E 37 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.7743 (ttm-80) REVERT: E 57 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8591 (t) REVERT: E 95 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8687 (tm-30) REVERT: F 6 ARG cc_start: 0.8451 (tpt90) cc_final: 0.8014 (tpt90) REVERT: F 9 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8188 (mt0) REVERT: F 10 MET cc_start: 0.9287 (tpp) cc_final: 0.9056 (mmm) REVERT: F 24 MET cc_start: 0.8547 (tpt) cc_final: 0.8271 (tpp) REVERT: F 58 MET cc_start: 0.9182 (mmm) cc_final: 0.8933 (tpp) REVERT: F 69 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7335 (pt) REVERT: F 81 ASP cc_start: 0.8856 (t0) cc_final: 0.8357 (t0) REVERT: F 95 GLU cc_start: 0.8388 (tp30) cc_final: 0.7919 (tp30) REVERT: G 150 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8687 (tt) REVERT: G 204 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8306 (ttm-80) REVERT: H 5 ASP cc_start: 0.5574 (m-30) cc_final: 0.5218 (m-30) REVERT: H 9 GLN cc_start: 0.8272 (mt0) cc_final: 0.7812 (mp10) REVERT: H 78 LYS cc_start: 0.7906 (ptmt) cc_final: 0.7324 (pttm) outliers start: 107 outliers final: 58 residues processed: 260 average time/residue: 1.1739 time to fit residues: 344.5858 Evaluate side-chains 215 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 454 ASP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 145 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN D 569 ASN D 619 ASN E 160 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN H 149 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.155616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080764 restraints weight = 35361.519| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.41 r_work: 0.2985 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18432 Z= 0.278 Angle : 0.653 9.676 24833 Z= 0.341 Chirality : 0.043 0.176 2768 Planarity : 0.004 0.051 3018 Dihedral : 11.818 89.180 2828 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.71 % Favored : 96.06 % Rotamer: Outliers : 5.83 % Allowed : 20.52 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2235 helix: 2.00 (0.14), residues: 1337 sheet: -2.49 (0.36), residues: 125 loop : -1.60 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 766 HIS 0.004 0.001 HIS F 205 PHE 0.019 0.002 PHE H 127 TYR 0.017 0.002 TYR C 647 ARG 0.013 0.001 ARG B 743 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 1122) hydrogen bonds : angle 4.54649 ( 3240) SS BOND : bond 0.00371 ( 12) SS BOND : angle 1.67684 ( 24) covalent geometry : bond 0.00645 (18420) covalent geometry : angle 0.65151 (24809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 164 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: A 408 MET cc_start: 0.8086 (mmm) cc_final: 0.7727 (mmt) REVERT: A 503 MET cc_start: 0.6401 (ttm) cc_final: 0.6025 (ptm) REVERT: A 759 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5769 (mt) REVERT: B 408 MET cc_start: 0.6832 (mpp) cc_final: 0.5105 (pp-130) REVERT: B 586 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8389 (mmm160) REVERT: C 414 MET cc_start: 0.7069 (mtm) cc_final: 0.6039 (ptt) REVERT: C 463 MET cc_start: 0.3465 (mpp) cc_final: 0.2230 (tpp) REVERT: C 503 MET cc_start: 0.5680 (tmm) cc_final: 0.5260 (tmm) REVERT: C 770 LYS cc_start: 0.0182 (OUTLIER) cc_final: -0.0141 (mptt) REVERT: D 414 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5306 (pmm) REVERT: D 620 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7973 (tp) REVERT: E 5 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5420 (p0) REVERT: E 32 TYR cc_start: 0.9013 (m-80) cc_final: 0.8786 (m-10) REVERT: E 37 ARG cc_start: 0.8582 (ttm-80) cc_final: 0.7673 (ttm-80) REVERT: E 56 GLU cc_start: 0.7566 (pp20) cc_final: 0.7355 (pp20) REVERT: E 57 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8576 (t) REVERT: E 174 TYR cc_start: 0.9000 (p90) cc_final: 0.8676 (p90) REVERT: F 6 ARG cc_start: 0.8428 (tpt90) cc_final: 0.8013 (tpt90) REVERT: F 9 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8172 (mt0) REVERT: F 69 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7286 (pp) REVERT: F 81 ASP cc_start: 0.8892 (t0) cc_final: 0.8434 (t0) REVERT: F 95 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: G 150 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8710 (tt) REVERT: G 191 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8858 (mm-30) REVERT: G 207 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: H 5 ASP cc_start: 0.5641 (m-30) cc_final: 0.5376 (m-30) REVERT: H 9 GLN cc_start: 0.8145 (mt0) cc_final: 0.7584 (mp10) REVERT: H 78 LYS cc_start: 0.7998 (ptmt) cc_final: 0.7471 (pttm) REVERT: H 203 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8879 (t0) outliers start: 106 outliers final: 60 residues processed: 248 average time/residue: 1.1352 time to fit residues: 319.1067 Evaluate side-chains 215 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 143 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 150 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 619 ASN E 160 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.152431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077530 restraints weight = 36289.301| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.45 r_work: 0.2935 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.079 18432 Z= 0.470 Angle : 0.804 12.624 24833 Z= 0.419 Chirality : 0.049 0.214 2768 Planarity : 0.005 0.050 3018 Dihedral : 12.103 98.472 2822 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.23 % Favored : 94.54 % Rotamer: Outliers : 7.04 % Allowed : 20.52 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2235 helix: 1.66 (0.14), residues: 1336 sheet: -2.59 (0.39), residues: 105 loop : -1.61 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 766 HIS 0.006 0.001 HIS G 205 PHE 0.025 0.003 PHE E 107 TYR 0.034 0.002 TYR D 732 ARG 0.007 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 1122) hydrogen bonds : angle 4.92158 ( 3240) SS BOND : bond 0.00653 ( 12) SS BOND : angle 2.68908 ( 24) covalent geometry : bond 0.01088 (18420) covalent geometry : angle 0.80051 (24809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 154 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8255 (mmm) cc_final: 0.7950 (mmt) REVERT: A 496 MET cc_start: 0.7475 (mmm) cc_final: 0.7094 (tmt) REVERT: A 756 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5826 (pp30) REVERT: B 408 MET cc_start: 0.6708 (mpp) cc_final: 0.4809 (pp-130) REVERT: B 503 MET cc_start: 0.6231 (pp-130) cc_final: 0.5719 (ppp) REVERT: B 586 ARG cc_start: 0.9128 (mmm-85) cc_final: 0.8385 (mmm160) REVERT: C 414 MET cc_start: 0.7183 (mtm) cc_final: 0.6170 (ptt) REVERT: C 647 TYR cc_start: 0.2422 (p90) cc_final: 0.1523 (p90) REVERT: C 674 MET cc_start: 0.4943 (mtt) cc_final: 0.4435 (mtp) REVERT: C 770 LYS cc_start: 0.0070 (OUTLIER) cc_final: -0.0254 (mptt) REVERT: D 414 MET cc_start: 0.6121 (mtm) cc_final: 0.5420 (pmm) REVERT: D 545 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7377 (mtp180) REVERT: E 5 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5862 (p0) REVERT: E 32 TYR cc_start: 0.9013 (m-80) cc_final: 0.8740 (m-10) REVERT: E 37 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: E 57 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8169 (t) REVERT: E 174 TYR cc_start: 0.9085 (p90) cc_final: 0.8822 (p90) REVERT: F 9 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8277 (mm110) REVERT: F 10 MET cc_start: 0.9318 (mmm) cc_final: 0.9045 (mmm) REVERT: F 81 ASP cc_start: 0.8846 (t0) cc_final: 0.8429 (t0) REVERT: F 95 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: G 95 GLU cc_start: 0.8999 (tp30) cc_final: 0.8704 (tm-30) REVERT: G 150 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8768 (tt) REVERT: G 205 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8650 (m170) REVERT: H 9 GLN cc_start: 0.8222 (mt0) cc_final: 0.7744 (mp10) REVERT: H 128 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7377 (m-80) outliers start: 128 outliers final: 68 residues processed: 256 average time/residue: 1.1568 time to fit residues: 338.0499 Evaluate side-chains 220 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 143 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 816 TYR Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 174 TYR Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 205 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 127 optimal weight: 30.0000 chunk 164 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN D 619 ASN E 160 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.155016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.080773 restraints weight = 35981.037| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.37 r_work: 0.2992 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 18432 Z= 0.285 Angle : 0.675 12.686 24833 Z= 0.350 Chirality : 0.044 0.206 2768 Planarity : 0.004 0.049 3018 Dihedral : 11.657 91.433 2816 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.07 % Favored : 95.70 % Rotamer: Outliers : 5.50 % Allowed : 22.28 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2235 helix: 2.02 (0.14), residues: 1335 sheet: -2.54 (0.38), residues: 118 loop : -1.59 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 766 HIS 0.006 0.001 HIS E 60 PHE 0.017 0.002 PHE H 127 TYR 0.022 0.002 TYR C 711 ARG 0.007 0.001 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 1122) hydrogen bonds : angle 4.57851 ( 3240) SS BOND : bond 0.00533 ( 12) SS BOND : angle 2.30241 ( 24) covalent geometry : bond 0.00665 (18420) covalent geometry : angle 0.67131 (24809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 159 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8232 (mmm) cc_final: 0.7972 (mmt) REVERT: A 495 PHE cc_start: 0.7385 (p90) cc_final: 0.6862 (p90) REVERT: A 496 MET cc_start: 0.7096 (mmm) cc_final: 0.6669 (tmt) REVERT: A 670 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7011 (mmm) REVERT: A 756 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6027 (pp30) REVERT: B 503 MET cc_start: 0.6157 (pp-130) cc_final: 0.5842 (ppp) REVERT: B 586 ARG cc_start: 0.9138 (mmm-85) cc_final: 0.8424 (mmm160) REVERT: B 650 LEU cc_start: 0.2935 (OUTLIER) cc_final: 0.2521 (tm) REVERT: C 414 MET cc_start: 0.6325 (mtm) cc_final: 0.5544 (ptt) REVERT: C 463 MET cc_start: 0.2606 (mpt) cc_final: 0.1501 (tpp) REVERT: C 647 TYR cc_start: 0.2089 (p90) cc_final: 0.1509 (p90) REVERT: C 674 MET cc_start: 0.4105 (mtt) cc_final: 0.3853 (mtp) REVERT: D 414 MET cc_start: 0.6117 (mtm) cc_final: 0.5423 (pmm) REVERT: D 620 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8030 (tp) REVERT: E 5 ASP cc_start: 0.6096 (OUTLIER) cc_final: 0.5561 (p0) REVERT: E 32 TYR cc_start: 0.8869 (m-80) cc_final: 0.8540 (m-10) REVERT: E 37 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.7313 (ttm-80) REVERT: E 57 VAL cc_start: 0.9135 (OUTLIER) cc_final: 0.8718 (t) REVERT: E 70 GLU cc_start: 0.7898 (pp20) cc_final: 0.7682 (pp20) REVERT: E 174 TYR cc_start: 0.9083 (p90) cc_final: 0.8752 (p90) REVERT: F 6 ARG cc_start: 0.8481 (tpt90) cc_final: 0.8198 (tpt90) REVERT: F 9 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8009 (mm-40) REVERT: F 10 MET cc_start: 0.9352 (mmm) cc_final: 0.9040 (mmm) REVERT: F 81 ASP cc_start: 0.8866 (t0) cc_final: 0.8385 (t0) REVERT: F 95 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8205 (tp30) REVERT: G 98 LEU cc_start: 0.9094 (tp) cc_final: 0.8831 (tm) REVERT: G 150 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8744 (tt) REVERT: G 191 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8906 (mm-30) REVERT: G 205 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8580 (m170) REVERT: G 207 GLN cc_start: 0.8591 (pt0) cc_final: 0.8351 (pp30) REVERT: H 9 GLN cc_start: 0.8223 (mt0) cc_final: 0.7699 (mp10) REVERT: H 128 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: H 203 ASP cc_start: 0.9172 (OUTLIER) cc_final: 0.8727 (t0) outliers start: 100 outliers final: 63 residues processed: 236 average time/residue: 1.1687 time to fit residues: 312.9361 Evaluate side-chains 218 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 144 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 502 ILE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 150 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 110 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN C 726 ASN D 619 ASN E 160 ASN F 60 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.159724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086470 restraints weight = 35537.646| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.32 r_work: 0.3094 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18432 Z= 0.123 Angle : 0.596 12.576 24833 Z= 0.305 Chirality : 0.041 0.190 2768 Planarity : 0.004 0.050 3018 Dihedral : 10.661 89.847 2816 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.18 % Favored : 96.60 % Rotamer: Outliers : 3.85 % Allowed : 24.31 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.19), residues: 2235 helix: 2.56 (0.14), residues: 1333 sheet: -1.87 (0.39), residues: 137 loop : -1.49 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP B 460 HIS 0.004 0.001 HIS F 205 PHE 0.017 0.001 PHE D 495 TYR 0.024 0.001 TYR C 711 ARG 0.007 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 1122) hydrogen bonds : angle 4.14968 ( 3240) SS BOND : bond 0.00499 ( 12) SS BOND : angle 1.79421 ( 24) covalent geometry : bond 0.00275 (18420) covalent geometry : angle 0.59411 (24809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 189 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8199 (mmm) cc_final: 0.7944 (mmt) REVERT: A 670 MET cc_start: 0.7899 (mmt) cc_final: 0.7143 (mmm) REVERT: A 756 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.5692 (pp30) REVERT: B 407 MET cc_start: 0.7237 (ppp) cc_final: 0.6902 (ppp) REVERT: B 408 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.5135 (pp-130) REVERT: B 496 MET cc_start: 0.3888 (ptp) cc_final: 0.2494 (ppp) REVERT: B 586 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8224 (mmm160) REVERT: B 650 LEU cc_start: 0.2023 (OUTLIER) cc_final: 0.1510 (tm) REVERT: C 414 MET cc_start: 0.6491 (mtm) cc_final: 0.5890 (ptt) REVERT: C 463 MET cc_start: 0.2732 (mpt) cc_final: 0.1614 (tpp) REVERT: D 408 MET cc_start: 0.5813 (tpp) cc_final: 0.5554 (tpp) REVERT: D 414 MET cc_start: 0.6222 (mtm) cc_final: 0.5582 (pmm) REVERT: E 5 ASP cc_start: 0.5874 (OUTLIER) cc_final: 0.5409 (p0) REVERT: E 13 THR cc_start: 0.8692 (m) cc_final: 0.8307 (m) REVERT: E 32 TYR cc_start: 0.8929 (m-80) cc_final: 0.8594 (m-10) REVERT: E 37 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8395 (ttt90) REVERT: E 56 GLU cc_start: 0.7424 (pp20) cc_final: 0.7093 (pp20) REVERT: E 174 TYR cc_start: 0.9138 (p90) cc_final: 0.8892 (p90) REVERT: E 204 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8738 (mtp-110) REVERT: F 9 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8245 (mt0) REVERT: F 10 MET cc_start: 0.9272 (mmm) cc_final: 0.8959 (mmm) REVERT: F 81 ASP cc_start: 0.8783 (t0) cc_final: 0.8289 (t0) REVERT: F 95 GLU cc_start: 0.8622 (tp30) cc_final: 0.8175 (tp30) REVERT: G 32 TYR cc_start: 0.8700 (m-10) cc_final: 0.8480 (m-10) REVERT: G 56 GLU cc_start: 0.7349 (tp30) cc_final: 0.7122 (tp30) REVERT: G 60 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7850 (p90) REVERT: G 98 LEU cc_start: 0.9085 (tp) cc_final: 0.8874 (tm) REVERT: G 140 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8648 (mp) REVERT: G 191 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8862 (mm-30) REVERT: G 207 GLN cc_start: 0.8597 (pt0) cc_final: 0.8353 (pp30) REVERT: H 9 GLN cc_start: 0.8102 (mt0) cc_final: 0.7689 (mp10) REVERT: H 70 GLU cc_start: 0.7968 (pp20) cc_final: 0.7757 (pp20) REVERT: H 78 LYS cc_start: 0.8050 (ptmt) cc_final: 0.7755 (pttm) REVERT: H 203 ASP cc_start: 0.9206 (t0) cc_final: 0.8795 (t0) outliers start: 70 outliers final: 29 residues processed: 245 average time/residue: 1.1418 time to fit residues: 317.1962 Evaluate side-chains 202 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 191 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 209 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 619 ASN E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.156453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.082312 restraints weight = 35692.723| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.29 r_work: 0.3017 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18432 Z= 0.232 Angle : 0.689 10.744 24833 Z= 0.351 Chirality : 0.043 0.264 2768 Planarity : 0.004 0.048 3018 Dihedral : 10.834 89.608 2810 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.97 % Rotamer: Outliers : 3.74 % Allowed : 24.53 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2235 helix: 2.44 (0.14), residues: 1334 sheet: -2.17 (0.39), residues: 127 loop : -1.47 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP B 460 HIS 0.005 0.001 HIS E 60 PHE 0.015 0.002 PHE B 495 TYR 0.024 0.002 TYR C 711 ARG 0.007 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 1122) hydrogen bonds : angle 4.39748 ( 3240) SS BOND : bond 0.00615 ( 12) SS BOND : angle 2.87611 ( 24) covalent geometry : bond 0.00542 (18420) covalent geometry : angle 0.68390 (24809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 158 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.8093 (mpp) cc_final: 0.7801 (mpp) REVERT: A 408 MET cc_start: 0.8245 (mmm) cc_final: 0.7945 (mmt) REVERT: A 495 PHE cc_start: 0.7565 (p90) cc_final: 0.6992 (p90) REVERT: A 670 MET cc_start: 0.7898 (mmt) cc_final: 0.7200 (mmm) REVERT: A 756 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.5707 (pp30) REVERT: B 407 MET cc_start: 0.7246 (ppp) cc_final: 0.6897 (ppp) REVERT: B 408 MET cc_start: 0.6830 (mpm) cc_final: 0.4747 (pp-130) REVERT: B 496 MET cc_start: 0.3726 (ptp) cc_final: 0.2638 (ppp) REVERT: B 586 ARG cc_start: 0.9083 (mmm-85) cc_final: 0.8415 (mmm160) REVERT: B 650 LEU cc_start: 0.2544 (OUTLIER) cc_final: 0.2142 (tm) REVERT: B 721 MET cc_start: 0.8225 (ptm) cc_final: 0.7966 (ppp) REVERT: B 769 ASP cc_start: 0.7090 (t0) cc_final: 0.6760 (m-30) REVERT: C 414 MET cc_start: 0.6475 (mtm) cc_final: 0.5747 (ptt) REVERT: C 674 MET cc_start: 0.3892 (mtt) cc_final: 0.3554 (mtp) REVERT: D 408 MET cc_start: 0.5840 (tpp) cc_final: 0.5578 (tpp) REVERT: D 414 MET cc_start: 0.6336 (mtm) cc_final: 0.5734 (pmm) REVERT: E 5 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5748 (p0) REVERT: E 32 TYR cc_start: 0.9007 (m-80) cc_final: 0.8689 (m-10) REVERT: E 70 GLU cc_start: 0.8250 (pp20) cc_final: 0.7880 (pp20) REVERT: E 174 TYR cc_start: 0.9179 (p90) cc_final: 0.8938 (p90) REVERT: F 9 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8306 (mt0) REVERT: F 10 MET cc_start: 0.9364 (mmm) cc_final: 0.9079 (mmm) REVERT: F 81 ASP cc_start: 0.8812 (t0) cc_final: 0.8332 (t0) REVERT: F 95 GLU cc_start: 0.8584 (tp30) cc_final: 0.8130 (tp30) REVERT: G 58 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8362 (mmp) REVERT: G 60 HIS cc_start: 0.8330 (OUTLIER) cc_final: 0.7586 (p90) REVERT: G 98 LEU cc_start: 0.9106 (tp) cc_final: 0.8852 (tm) REVERT: G 140 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8798 (mp) REVERT: G 191 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8880 (mm-30) REVERT: G 205 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8519 (m170) REVERT: G 207 GLN cc_start: 0.8684 (pt0) cc_final: 0.8427 (pp30) REVERT: H 9 GLN cc_start: 0.8250 (mt0) cc_final: 0.7725 (mp10) REVERT: H 70 GLU cc_start: 0.8303 (pp20) cc_final: 0.8039 (pp20) REVERT: H 203 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8748 (t0) outliers start: 68 outliers final: 36 residues processed: 215 average time/residue: 1.0928 time to fit residues: 267.1830 Evaluate side-chains 195 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 203 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 48 optimal weight: 8.9990 chunk 171 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 191 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 619 ASN E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.158060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.084303 restraints weight = 35784.231| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.37 r_work: 0.3047 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18432 Z= 0.171 Angle : 0.655 10.958 24833 Z= 0.333 Chirality : 0.042 0.253 2768 Planarity : 0.004 0.048 3018 Dihedral : 10.521 89.035 2808 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.58 % Favored : 96.20 % Rotamer: Outliers : 2.81 % Allowed : 25.80 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 2235 helix: 2.55 (0.14), residues: 1330 sheet: -2.05 (0.38), residues: 147 loop : -1.44 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 460 HIS 0.004 0.001 HIS E 60 PHE 0.022 0.001 PHE D 623 TYR 0.023 0.001 TYR C 711 ARG 0.009 0.001 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1122) hydrogen bonds : angle 4.30401 ( 3240) SS BOND : bond 0.00529 ( 12) SS BOND : angle 2.42413 ( 24) covalent geometry : bond 0.00396 (18420) covalent geometry : angle 0.65108 (24809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7900 (mpp) cc_final: 0.7616 (mpp) REVERT: A 408 MET cc_start: 0.8273 (mmm) cc_final: 0.7986 (mmt) REVERT: A 670 MET cc_start: 0.7899 (mmt) cc_final: 0.7284 (mmm) REVERT: A 756 GLN cc_start: 0.6470 (OUTLIER) cc_final: 0.5715 (pp30) REVERT: B 407 MET cc_start: 0.7481 (ppp) cc_final: 0.7148 (ppp) REVERT: B 408 MET cc_start: 0.7062 (mpm) cc_final: 0.4888 (pp-130) REVERT: B 496 MET cc_start: 0.2723 (ptp) cc_final: 0.1867 (ppp) REVERT: B 586 ARG cc_start: 0.9074 (mmm-85) cc_final: 0.8434 (mmm160) REVERT: B 650 LEU cc_start: 0.2401 (OUTLIER) cc_final: 0.1991 (tm) REVERT: C 414 MET cc_start: 0.6445 (mtm) cc_final: 0.5771 (ptt) REVERT: D 408 MET cc_start: 0.5488 (tpp) cc_final: 0.5269 (tpp) REVERT: D 414 MET cc_start: 0.6345 (mtm) cc_final: 0.5751 (pmm) REVERT: E 5 ASP cc_start: 0.6031 (OUTLIER) cc_final: 0.5585 (p0) REVERT: E 32 TYR cc_start: 0.9023 (m-80) cc_final: 0.8697 (m-80) REVERT: E 58 MET cc_start: 0.8754 (tpt) cc_final: 0.8553 (tpp) REVERT: E 70 GLU cc_start: 0.8139 (pp20) cc_final: 0.7901 (pp20) REVERT: E 204 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8775 (mtp-110) REVERT: F 9 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8304 (mt0) REVERT: F 10 MET cc_start: 0.9312 (mmm) cc_final: 0.9057 (mmm) REVERT: F 81 ASP cc_start: 0.8776 (t0) cc_final: 0.8289 (t0) REVERT: F 95 GLU cc_start: 0.8574 (tp30) cc_final: 0.8130 (tp30) REVERT: G 58 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8385 (mmp) REVERT: G 60 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.7757 (p90) REVERT: G 98 LEU cc_start: 0.9057 (tp) cc_final: 0.8830 (tm) REVERT: G 140 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8743 (mp) REVERT: G 191 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8896 (mm-30) REVERT: G 207 GLN cc_start: 0.8627 (pt0) cc_final: 0.8391 (pp30) REVERT: H 9 GLN cc_start: 0.8217 (mt0) cc_final: 0.7702 (mp10) REVERT: H 70 GLU cc_start: 0.8213 (pp20) cc_final: 0.7902 (pp20) REVERT: H 203 ASP cc_start: 0.9215 (t0) cc_final: 0.8821 (t0) outliers start: 51 outliers final: 30 residues processed: 204 average time/residue: 1.0968 time to fit residues: 254.7814 Evaluate side-chains 192 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 168 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 619 ASN E 160 ASN F 60 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.159919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086502 restraints weight = 34865.510| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 3.32 r_work: 0.3087 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18432 Z= 0.135 Angle : 0.646 12.187 24833 Z= 0.326 Chirality : 0.041 0.196 2768 Planarity : 0.004 0.049 3018 Dihedral : 10.129 88.225 2804 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.45 % Favored : 96.33 % Rotamer: Outliers : 2.48 % Allowed : 26.07 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2235 helix: 2.64 (0.14), residues: 1334 sheet: -2.11 (0.42), residues: 122 loop : -1.46 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP D 766 HIS 0.003 0.001 HIS E 60 PHE 0.023 0.001 PHE D 659 TYR 0.022 0.001 TYR C 711 ARG 0.009 0.001 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 1122) hydrogen bonds : angle 4.22748 ( 3240) SS BOND : bond 0.00392 ( 12) SS BOND : angle 1.88931 ( 24) covalent geometry : bond 0.00304 (18420) covalent geometry : angle 0.64359 (24809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8210 (mmm) cc_final: 0.7947 (mmt) REVERT: A 670 MET cc_start: 0.7955 (mmt) cc_final: 0.7275 (mmm) REVERT: A 756 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5703 (pp30) REVERT: B 407 MET cc_start: 0.7579 (ppp) cc_final: 0.7256 (ppp) REVERT: B 408 MET cc_start: 0.7016 (mpm) cc_final: 0.4751 (pp-130) REVERT: B 496 MET cc_start: 0.2580 (ptp) cc_final: 0.1811 (ppp) REVERT: B 586 ARG cc_start: 0.9031 (mmm-85) cc_final: 0.8371 (mmm160) REVERT: B 650 LEU cc_start: 0.2233 (OUTLIER) cc_final: 0.1834 (tm) REVERT: B 714 GLN cc_start: 0.8337 (tp-100) cc_final: 0.8122 (tm-30) REVERT: C 414 MET cc_start: 0.6539 (mtm) cc_final: 0.5845 (ptt) REVERT: C 463 MET cc_start: 0.2011 (mmt) cc_final: 0.1644 (mmt) REVERT: D 414 MET cc_start: 0.6370 (mtm) cc_final: 0.5739 (pmm) REVERT: D 659 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8331 (t80) REVERT: E 5 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5448 (p0) REVERT: E 13 THR cc_start: 0.8754 (m) cc_final: 0.8376 (t) REVERT: E 32 TYR cc_start: 0.9052 (m-80) cc_final: 0.8745 (m-80) REVERT: E 58 MET cc_start: 0.8849 (tpt) cc_final: 0.8593 (tpp) REVERT: E 70 GLU cc_start: 0.8110 (pp20) cc_final: 0.7903 (pp20) REVERT: E 174 TYR cc_start: 0.9004 (p90) cc_final: 0.8761 (p90) REVERT: E 204 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8742 (mtp-110) REVERT: F 9 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8312 (mt0) REVERT: F 10 MET cc_start: 0.9359 (mmm) cc_final: 0.9082 (mmm) REVERT: F 81 ASP cc_start: 0.8748 (t0) cc_final: 0.8230 (t0) REVERT: F 95 GLU cc_start: 0.8573 (tp30) cc_final: 0.8106 (tp30) REVERT: G 56 GLU cc_start: 0.7532 (tp30) cc_final: 0.7276 (tp30) REVERT: G 58 MET cc_start: 0.8757 (mmp) cc_final: 0.8360 (mmp) REVERT: G 98 LEU cc_start: 0.9066 (tp) cc_final: 0.8861 (tm) REVERT: G 140 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8707 (mp) REVERT: G 191 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8869 (mm-30) REVERT: G 207 GLN cc_start: 0.8623 (pt0) cc_final: 0.8350 (pp30) REVERT: H 9 GLN cc_start: 0.8198 (mt0) cc_final: 0.7670 (mp10) REVERT: H 70 GLU cc_start: 0.8216 (pp20) cc_final: 0.7886 (pp20) REVERT: H 203 ASP cc_start: 0.9190 (t0) cc_final: 0.8828 (t0) outliers start: 45 outliers final: 32 residues processed: 208 average time/residue: 1.1240 time to fit residues: 266.2493 Evaluate side-chains 199 residues out of total 1919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 658 PHE Chi-restraints excluded: chain D residue 659 PHE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 148 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 118 optimal weight: 0.0060 chunk 197 optimal weight: 0.7980 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 619 ASN E 160 ASN F 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.159176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.085381 restraints weight = 34851.179| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.34 r_work: 0.3066 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18432 Z= 0.155 Angle : 0.664 12.018 24833 Z= 0.335 Chirality : 0.042 0.210 2768 Planarity : 0.004 0.048 3018 Dihedral : 10.085 88.468 2804 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.47 % Rotamer: Outliers : 2.26 % Allowed : 26.57 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.19), residues: 2235 helix: 2.62 (0.14), residues: 1333 sheet: -2.12 (0.42), residues: 123 loop : -1.44 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP D 766 HIS 0.004 0.001 HIS E 60 PHE 0.018 0.001 PHE D 623 TYR 0.023 0.001 TYR C 711 ARG 0.009 0.001 ARG G 204 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 1122) hydrogen bonds : angle 4.28697 ( 3240) SS BOND : bond 0.00387 ( 12) SS BOND : angle 1.51028 ( 24) covalent geometry : bond 0.00359 (18420) covalent geometry : angle 0.66250 (24809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16111.47 seconds wall clock time: 277 minutes 13.56 seconds (16633.56 seconds total)