Starting phenix.real_space_refine on Sun Apr 14 14:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptr_13634/04_2024/7ptr_13634.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptr_13634/04_2024/7ptr_13634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptr_13634/04_2024/7ptr_13634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptr_13634/04_2024/7ptr_13634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptr_13634/04_2024/7ptr_13634.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ptr_13634/04_2024/7ptr_13634.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 18 9.91 5 S 30 5.16 5 C 19014 2.51 5 N 4998 2.21 5 O 7644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31704 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "B" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "C" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "D" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "E" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "F" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5248 Classifications: {'peptide': 725} Link IDs: {'PTRANS': 15, 'TRANS': 709} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 36 Unusual residues: {' CA': 3, 'BGC': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 16.16, per 1000 atoms: 0.51 Number of scatterers: 31704 At special positions: 0 Unit cell: (205.7, 227.7, 117.7, 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) Ca 18 19.99 S 30 16.00 O 7644 8.00 N 4998 7.00 C 19014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.84 Conformation dependent library (CDL) restraints added in 6.6 seconds 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7752 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 72 sheets defined 14.1% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.605A pdb=" N GLU A 83 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY A 149 " --> pdb=" O SER A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 149' Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL A 369 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.657A pdb=" N ASP A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 526 Processing helix chain 'A' and resid 606 through 618 removed outlier: 3.684A pdb=" N GLY A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 641 " --> pdb=" O GLU A 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 637 through 641' Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU B 83 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY B 149 " --> pdb=" O SER B 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL B 369 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 454 through 461 Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.656A pdb=" N ASP B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 477' Processing helix chain 'B' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 526 Processing helix chain 'B' and resid 606 through 618 removed outlier: 3.685A pdb=" N GLY B 612 " --> pdb=" O ASN B 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 613 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 617 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 636 Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA B 640 " --> pdb=" O ASP B 637 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 641' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU C 83 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 149 removed outlier: 3.762A pdb=" N GLY C 149 " --> pdb=" O SER C 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 149' Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL C 369 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 454 through 461 Processing helix chain 'C' and resid 473 through 477 removed outlier: 3.657A pdb=" N ASP C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 477' Processing helix chain 'C' and resid 489 through 496 removed outlier: 3.557A pdb=" N GLY C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 526 Processing helix chain 'C' and resid 606 through 618 removed outlier: 3.684A pdb=" N GLY C 612 " --> pdb=" O ASN C 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 613 " --> pdb=" O ASP C 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 616 " --> pdb=" O GLY C 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 617 " --> pdb=" O TYR C 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 636 Processing helix chain 'C' and resid 637 through 641 removed outlier: 3.738A pdb=" N ALA C 640 " --> pdb=" O ASP C 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 641 " --> pdb=" O GLU C 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 637 through 641' Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU D 83 " --> pdb=" O GLY D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY D 149 " --> pdb=" O SER D 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL D 369 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 454 through 461 Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.656A pdb=" N ASP D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 473 through 477' Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 526 Processing helix chain 'D' and resid 606 through 618 removed outlier: 3.683A pdb=" N GLY D 612 " --> pdb=" O ASN D 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 613 " --> pdb=" O ASP D 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR D 616 " --> pdb=" O GLY D 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 617 " --> pdb=" O TYR D 613 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 636 Processing helix chain 'D' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA D 640 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 641 " --> pdb=" O GLU D 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 637 through 641' Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU E 83 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY E 149 " --> pdb=" O SER E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 149' Processing helix chain 'E' and resid 177 through 182 Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 366 through 370 removed outlier: 3.624A pdb=" N VAL E 369 " --> pdb=" O THR E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 452 No H-bonds generated for 'chain 'E' and resid 450 through 452' Processing helix chain 'E' and resid 454 through 461 Processing helix chain 'E' and resid 473 through 477 removed outlier: 3.656A pdb=" N ASP E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 473 through 477' Processing helix chain 'E' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 526 Processing helix chain 'E' and resid 606 through 618 removed outlier: 3.685A pdb=" N GLY E 612 " --> pdb=" O ASN E 608 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR E 613 " --> pdb=" O ASP E 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR E 616 " --> pdb=" O GLY E 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 617 " --> pdb=" O TYR E 613 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP E 618 " --> pdb=" O LEU E 614 " (cutoff:3.500A) Processing helix chain 'E' and resid 623 through 636 Processing helix chain 'E' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA E 640 " --> pdb=" O ASP E 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 641 " --> pdb=" O GLU E 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 637 through 641' Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.604A pdb=" N GLU F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 149 removed outlier: 3.761A pdb=" N GLY F 149 " --> pdb=" O SER F 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 146 through 149' Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 366 through 370 removed outlier: 3.623A pdb=" N VAL F 369 " --> pdb=" O THR F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 454 through 461 Processing helix chain 'F' and resid 473 through 477 removed outlier: 3.657A pdb=" N ASP F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 473 through 477' Processing helix chain 'F' and resid 489 through 496 removed outlier: 3.558A pdb=" N GLY F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 526 Processing helix chain 'F' and resid 606 through 618 removed outlier: 3.684A pdb=" N GLY F 612 " --> pdb=" O ASN F 608 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR F 613 " --> pdb=" O ASP F 609 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR F 616 " --> pdb=" O GLY F 612 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 617 " --> pdb=" O TYR F 613 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP F 618 " --> pdb=" O LEU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 636 Processing helix chain 'F' and resid 637 through 641 removed outlier: 3.739A pdb=" N ALA F 640 " --> pdb=" O ASP F 637 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 641 " --> pdb=" O GLU F 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 637 through 641' Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY A 103 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 4.197A pdb=" N VAL A 165 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 255 removed outlier: 3.578A pdb=" N VAL A 254 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 375 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP A 355 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASP A 278 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 271 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 334 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR A 301 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL A 401 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 396 Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 396 Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 514 removed outlier: 4.273A pdb=" N GLY A 527 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 531 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP A 568 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY A 533 " --> pdb=" O ASP A 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP A 566 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 552 through 558 Processing sheet with id=AB2, first strand: chain 'A' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE A 659 " --> pdb=" O SER A 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER A 686 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL A 675 " --> pdb=" O VAL A 754 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY B 103 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 131 Processing sheet with id=AB6, first strand: chain 'B' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL B 165 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 246 through 249 Processing sheet with id=AB8, first strand: chain 'B' and resid 253 through 255 removed outlier: 3.579A pdb=" N VAL B 254 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 375 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP B 355 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP B 278 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN B 271 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU B 334 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR B 301 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 387 through 388 removed outlier: 5.854A pdb=" N VAL B 401 " --> pdb=" O ASP B 446 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 393 through 396 Processing sheet with id=AC2, first strand: chain 'B' and resid 393 through 396 Processing sheet with id=AC3, first strand: chain 'B' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY B 527 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 531 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP B 568 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY B 533 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 566 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 552 through 558 Processing sheet with id=AC5, first strand: chain 'B' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE B 659 " --> pdb=" O SER B 686 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER B 686 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL B 675 " --> pdb=" O VAL B 754 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY C 103 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 125 through 131 Processing sheet with id=AC9, first strand: chain 'C' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL C 165 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 246 through 249 Processing sheet with id=AD2, first strand: chain 'C' and resid 253 through 255 removed outlier: 3.579A pdb=" N VAL C 254 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 375 " --> pdb=" O VAL C 358 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP C 355 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP C 278 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN C 271 " --> pdb=" O ILE C 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 334 " --> pdb=" O THR C 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR C 301 " --> pdb=" O GLU C 334 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 387 through 388 removed outlier: 5.854A pdb=" N VAL C 401 " --> pdb=" O ASP C 446 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 393 through 396 Processing sheet with id=AD5, first strand: chain 'C' and resid 393 through 396 Processing sheet with id=AD6, first strand: chain 'C' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY C 527 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 531 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP C 568 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY C 533 " --> pdb=" O ASP C 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP C 566 " --> pdb=" O GLY C 533 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 552 through 558 Processing sheet with id=AD8, first strand: chain 'C' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE C 659 " --> pdb=" O SER C 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER C 686 " --> pdb=" O ILE C 659 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL C 675 " --> pdb=" O VAL C 754 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY D 103 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 125 through 131 Processing sheet with id=AE3, first strand: chain 'D' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL D 165 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 246 through 249 Processing sheet with id=AE5, first strand: chain 'D' and resid 253 through 255 removed outlier: 3.579A pdb=" N VAL D 254 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 375 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 355 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP D 278 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN D 271 " --> pdb=" O ILE D 335 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU D 334 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR D 301 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL D 401 " --> pdb=" O ASP D 446 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 393 through 396 Processing sheet with id=AE8, first strand: chain 'D' and resid 393 through 396 Processing sheet with id=AE9, first strand: chain 'D' and resid 513 through 514 removed outlier: 4.273A pdb=" N GLY D 527 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE D 531 " --> pdb=" O ASP D 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP D 568 " --> pdb=" O ILE D 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY D 533 " --> pdb=" O ASP D 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP D 566 " --> pdb=" O GLY D 533 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 552 through 558 Processing sheet with id=AF2, first strand: chain 'D' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE D 659 " --> pdb=" O SER D 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 686 " --> pdb=" O ILE D 659 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 675 through 676 removed outlier: 5.750A pdb=" N VAL D 675 " --> pdb=" O VAL D 754 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY E 103 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AF6, first strand: chain 'E' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL E 165 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 246 through 249 Processing sheet with id=AF8, first strand: chain 'E' and resid 253 through 255 removed outlier: 3.578A pdb=" N VAL E 254 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN E 375 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP E 355 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP E 278 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 271 " --> pdb=" O ILE E 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU E 334 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR E 301 " --> pdb=" O GLU E 334 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL E 401 " --> pdb=" O ASP E 446 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 393 through 396 Processing sheet with id=AG2, first strand: chain 'E' and resid 393 through 396 Processing sheet with id=AG3, first strand: chain 'E' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY E 527 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 531 " --> pdb=" O ASP E 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP E 568 " --> pdb=" O ILE E 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY E 533 " --> pdb=" O ASP E 566 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP E 566 " --> pdb=" O GLY E 533 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 552 through 558 Processing sheet with id=AG5, first strand: chain 'E' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE E 659 " --> pdb=" O SER E 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER E 686 " --> pdb=" O ILE E 659 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL E 675 " --> pdb=" O VAL E 754 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 56 through 57 removed outlier: 3.646A pdb=" N GLY F 103 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 125 through 131 Processing sheet with id=AG9, first strand: chain 'F' and resid 142 through 144 removed outlier: 4.198A pdb=" N VAL F 165 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 246 through 249 Processing sheet with id=AH2, first strand: chain 'F' and resid 253 through 255 removed outlier: 3.578A pdb=" N VAL F 254 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 375 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP F 355 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP F 278 " --> pdb=" O ASP F 355 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN F 271 " --> pdb=" O ILE F 335 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU F 334 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR F 301 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 387 through 388 removed outlier: 5.855A pdb=" N VAL F 401 " --> pdb=" O ASP F 446 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 393 through 396 Processing sheet with id=AH5, first strand: chain 'F' and resid 393 through 396 Processing sheet with id=AH6, first strand: chain 'F' and resid 513 through 514 removed outlier: 4.272A pdb=" N GLY F 527 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 531 " --> pdb=" O ASP F 568 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASP F 568 " --> pdb=" O ILE F 531 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY F 533 " --> pdb=" O ASP F 566 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ASP F 566 " --> pdb=" O GLY F 533 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 552 through 558 Processing sheet with id=AH8, first strand: chain 'F' and resid 657 through 664 removed outlier: 5.153A pdb=" N ILE F 659 " --> pdb=" O SER F 686 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER F 686 " --> pdb=" O ILE F 659 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F' and resid 675 through 676 removed outlier: 5.749A pdb=" N VAL F 675 " --> pdb=" O VAL F 754 " (cutoff:3.500A) 1242 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: 15.58 Time building geometry restraints manager: 13.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11391 1.34 - 1.46: 4670 1.46 - 1.57: 15865 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 31986 Sorted by residual: bond pdb=" C5 BGC D 905 " pdb=" O5 BGC D 905 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" C5 BGC E 904 " pdb=" O5 BGC E 904 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 BGC F 905 " pdb=" O5 BGC F 905 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 BGC C 905 " pdb=" O5 BGC C 905 " ideal model delta sigma weight residual 1.411 1.437 -0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C5 BGC D 904 " pdb=" O5 BGC D 904 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.61e+00 ... (remaining 31981 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 429 106.71 - 113.53: 18573 113.53 - 120.36: 10547 120.36 - 127.18: 14053 127.18 - 134.01: 138 Bond angle restraints: 43740 Sorted by residual: angle pdb=" N TYR D 663 " pdb=" CA TYR D 663 " pdb=" C TYR D 663 " ideal model delta sigma weight residual 108.11 111.60 -3.49 1.29e+00 6.01e-01 7.33e+00 angle pdb=" N TYR C 663 " pdb=" CA TYR C 663 " pdb=" C TYR C 663 " ideal model delta sigma weight residual 108.11 111.59 -3.48 1.29e+00 6.01e-01 7.28e+00 angle pdb=" N TYR E 663 " pdb=" CA TYR E 663 " pdb=" C TYR E 663 " ideal model delta sigma weight residual 108.11 111.58 -3.47 1.29e+00 6.01e-01 7.24e+00 angle pdb=" N TYR A 663 " pdb=" CA TYR A 663 " pdb=" C TYR A 663 " ideal model delta sigma weight residual 108.11 111.57 -3.46 1.29e+00 6.01e-01 7.19e+00 angle pdb=" N TYR F 663 " pdb=" CA TYR F 663 " pdb=" C TYR F 663 " ideal model delta sigma weight residual 108.11 111.56 -3.45 1.29e+00 6.01e-01 7.14e+00 ... (remaining 43735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 18406 17.05 - 34.10: 639 34.10 - 51.15: 59 51.15 - 68.20: 18 68.20 - 85.25: 42 Dihedral angle restraints: 19164 sinusoidal: 6972 harmonic: 12192 Sorted by residual: dihedral pdb=" CB GLU E 756 " pdb=" CG GLU E 756 " pdb=" CD GLU E 756 " pdb=" OE1 GLU E 756 " ideal model delta sinusoidal sigma weight residual 0.00 -85.25 85.25 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" CB GLU F 756 " pdb=" CG GLU F 756 " pdb=" CD GLU F 756 " pdb=" OE1 GLU F 756 " ideal model delta sinusoidal sigma weight residual 0.00 -85.24 85.24 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" CB GLU D 756 " pdb=" CG GLU D 756 " pdb=" CD GLU D 756 " pdb=" OE1 GLU D 756 " ideal model delta sinusoidal sigma weight residual 0.00 -85.24 85.24 1 3.00e+01 1.11e-03 9.78e+00 ... (remaining 19161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3403 0.029 - 0.058: 1171 0.058 - 0.088: 351 0.088 - 0.117: 368 0.117 - 0.146: 89 Chirality restraints: 5382 Sorted by residual: chirality pdb=" CA ILE F 130 " pdb=" N ILE F 130 " pdb=" C ILE F 130 " pdb=" CB ILE F 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ILE C 130 " pdb=" N ILE C 130 " pdb=" C ILE C 130 " pdb=" CB ILE C 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE E 130 " pdb=" N ILE E 130 " pdb=" C ILE E 130 " pdb=" CB ILE E 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 5379 not shown) Planarity restraints: 5940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 171 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO F 172 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 172 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 171 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 172 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 172 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 172 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 171 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO D 172 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.025 5.00e-02 4.00e+02 ... (remaining 5937 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2986 2.74 - 3.28: 33061 3.28 - 3.82: 51115 3.82 - 4.36: 61041 4.36 - 4.90: 105420 Nonbonded interactions: 253623 Sorted by model distance: nonbonded pdb=" OG1 THR C 701 " pdb=" OG1 THR C 737 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR F 701 " pdb=" OG1 THR F 737 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR B 701 " pdb=" OG1 THR B 737 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR D 701 " pdb=" OG1 THR D 737 " model vdw 2.196 2.440 nonbonded pdb=" OG1 THR A 701 " pdb=" OG1 THR A 737 " model vdw 2.196 2.440 ... (remaining 253618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 4.190 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: 0.040 Extract box with map and model: 14.800 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 88.820 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 114.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.002 0.030 31986 Z= 0.135 Angle : 0.472 4.767 43740 Z= 0.267 Chirality : 0.043 0.146 5382 Planarity : 0.003 0.045 5940 Dihedral : 9.734 85.249 11412 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.13), residues: 4338 helix: 0.50 (0.30), residues: 354 sheet: 0.21 (0.14), residues: 1314 loop : -0.20 (0.12), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 716 HIS 0.002 0.001 HIS C 273 PHE 0.005 0.001 PHE F 514 TYR 0.007 0.001 TYR D 663 ARG 0.001 0.000 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ASP cc_start: 0.7750 (p0) cc_final: 0.7507 (p0) REVERT: B 455 ASP cc_start: 0.8302 (m-30) cc_final: 0.8039 (t0) REVERT: C 208 MET cc_start: 0.8279 (mmm) cc_final: 0.7937 (mmt) REVERT: C 249 LEU cc_start: 0.8675 (mt) cc_final: 0.8463 (mt) REVERT: C 455 ASP cc_start: 0.8155 (m-30) cc_final: 0.7867 (t0) REVERT: D 355 ASP cc_start: 0.7765 (p0) cc_final: 0.7523 (p0) REVERT: D 455 ASP cc_start: 0.8126 (m-30) cc_final: 0.7833 (t0) REVERT: E 455 ASP cc_start: 0.8324 (m-30) cc_final: 0.8056 (t0) REVERT: F 208 MET cc_start: 0.8265 (mmm) cc_final: 0.7902 (mmt) REVERT: F 249 LEU cc_start: 0.8683 (mt) cc_final: 0.8474 (mt) REVERT: F 455 ASP cc_start: 0.8157 (m-30) cc_final: 0.7864 (t0) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.4326 time to fit residues: 177.5639 Evaluate side-chains 103 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 2.9990 chunk 327 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 252 optimal weight: 4.9990 chunk 392 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31986 Z= 0.262 Angle : 0.516 6.823 43740 Z= 0.281 Chirality : 0.045 0.222 5382 Planarity : 0.003 0.049 5940 Dihedral : 4.257 17.353 4854 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.50 % Allowed : 4.96 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.13), residues: 4338 helix: 0.55 (0.31), residues: 348 sheet: -0.26 (0.13), residues: 1440 loop : -0.19 (0.13), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 722 HIS 0.002 0.001 HIS A 582 PHE 0.012 0.002 PHE C 295 TYR 0.013 0.002 TYR B 157 ARG 0.003 0.000 ARG B 651 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8107 (m-30) cc_final: 0.7793 (t0) REVERT: C 455 ASP cc_start: 0.8092 (m-30) cc_final: 0.7821 (t0) REVERT: D 455 ASP cc_start: 0.7993 (m-30) cc_final: 0.7629 (t0) REVERT: E 455 ASP cc_start: 0.8142 (m-30) cc_final: 0.7825 (t0) REVERT: F 455 ASP cc_start: 0.8090 (m-30) cc_final: 0.7815 (t0) outliers start: 18 outliers final: 3 residues processed: 129 average time/residue: 0.4136 time to fit residues: 92.1194 Evaluate side-chains 101 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 393 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 350 optimal weight: 5.9990 chunk 389 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 31986 Z= 0.302 Angle : 0.525 6.304 43740 Z= 0.286 Chirality : 0.045 0.180 5382 Planarity : 0.003 0.046 5940 Dihedral : 4.550 19.298 4854 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.87 % Allowed : 6.95 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.13), residues: 4338 helix: 0.16 (0.30), residues: 348 sheet: -0.30 (0.13), residues: 1434 loop : -0.38 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 722 HIS 0.003 0.001 HIS D 582 PHE 0.016 0.002 PHE C 295 TYR 0.013 0.002 TYR E 157 ARG 0.002 0.000 ARG E 578 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 355 ASP cc_start: 0.8291 (p0) cc_final: 0.8090 (p0) REVERT: B 455 ASP cc_start: 0.8240 (m-30) cc_final: 0.7894 (t0) REVERT: C 455 ASP cc_start: 0.8130 (m-30) cc_final: 0.7871 (t0) REVERT: D 455 ASP cc_start: 0.8108 (m-30) cc_final: 0.7724 (t0) REVERT: E 355 ASP cc_start: 0.8301 (p0) cc_final: 0.8096 (p0) REVERT: E 455 ASP cc_start: 0.8248 (m-30) cc_final: 0.7898 (t0) REVERT: F 455 ASP cc_start: 0.8134 (m-30) cc_final: 0.7870 (t0) outliers start: 31 outliers final: 20 residues processed: 133 average time/residue: 0.4148 time to fit residues: 95.8596 Evaluate side-chains 118 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 401 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 8.9990 chunk 295 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 394 optimal weight: 4.9990 chunk 417 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 373 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31986 Z= 0.336 Angle : 0.539 6.577 43740 Z= 0.293 Chirality : 0.045 0.217 5382 Planarity : 0.003 0.046 5940 Dihedral : 4.728 19.765 4854 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.60 % Allowed : 7.68 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.80 (0.12), residues: 4338 helix: -0.04 (0.30), residues: 348 sheet: -0.49 (0.13), residues: 1470 loop : -0.55 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 722 HIS 0.003 0.002 HIS D 582 PHE 0.013 0.002 PHE D 295 TYR 0.013 0.002 TYR D 554 ARG 0.010 0.001 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 94 time to evaluate : 3.813 Fit side-chains revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8200 (m-30) cc_final: 0.7834 (t0) REVERT: B 578 ARG cc_start: 0.6702 (mmm160) cc_final: 0.6377 (mmm160) REVERT: D 455 ASP cc_start: 0.8124 (m-30) cc_final: 0.7752 (t0) REVERT: E 455 ASP cc_start: 0.8171 (m-30) cc_final: 0.7805 (t0) outliers start: 57 outliers final: 28 residues processed: 131 average time/residue: 0.3716 time to fit residues: 88.6090 Evaluate side-chains 118 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 3.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 172 optimal weight: 0.0170 chunk 356 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 374 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31986 Z= 0.290 Angle : 0.512 7.709 43740 Z= 0.279 Chirality : 0.044 0.160 5382 Planarity : 0.003 0.045 5940 Dihedral : 4.673 19.006 4854 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.16 % Allowed : 7.93 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.12), residues: 4338 helix: 0.00 (0.30), residues: 348 sheet: -0.50 (0.13), residues: 1458 loop : -0.64 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 722 HIS 0.003 0.001 HIS D 582 PHE 0.009 0.002 PHE D 295 TYR 0.013 0.002 TYR E 554 ARG 0.005 0.000 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 94 time to evaluate : 4.032 Fit side-chains REVERT: B 455 ASP cc_start: 0.8157 (m-30) cc_final: 0.7798 (t0) REVERT: B 578 ARG cc_start: 0.6701 (mmm160) cc_final: 0.6410 (mmm160) REVERT: D 455 ASP cc_start: 0.8104 (m-30) cc_final: 0.7733 (t0) REVERT: E 455 ASP cc_start: 0.8163 (m-30) cc_final: 0.7800 (t0) REVERT: E 578 ARG cc_start: 0.6688 (mmm160) cc_final: 0.6394 (mmm160) outliers start: 77 outliers final: 52 residues processed: 148 average time/residue: 0.3673 time to fit residues: 98.4044 Evaluate side-chains 141 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 89 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 660 ASP Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain E residue 660 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 630 LEU Chi-restraints excluded: chain F residue 660 ASP Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 9.9990 chunk 376 optimal weight: 0.6980 chunk 82 optimal weight: 0.0070 chunk 245 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 417 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 219 optimal weight: 0.0070 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31986 Z= 0.140 Angle : 0.450 6.432 43740 Z= 0.246 Chirality : 0.043 0.141 5382 Planarity : 0.003 0.045 5940 Dihedral : 4.163 16.605 4854 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.04 % Allowed : 10.00 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.13), residues: 4338 helix: 0.28 (0.31), residues: 348 sheet: -0.26 (0.13), residues: 1392 loop : -0.53 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 716 HIS 0.003 0.001 HIS B 273 PHE 0.008 0.001 PHE D 514 TYR 0.012 0.001 TYR E 554 ARG 0.006 0.000 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8071 (m-30) cc_final: 0.7748 (t0) REVERT: B 626 GLN cc_start: 0.8854 (mt0) cc_final: 0.8274 (mm110) REVERT: D 455 ASP cc_start: 0.7982 (m-30) cc_final: 0.7623 (t0) REVERT: E 455 ASP cc_start: 0.8075 (m-30) cc_final: 0.7749 (t0) outliers start: 37 outliers final: 20 residues processed: 126 average time/residue: 0.3807 time to fit residues: 87.1217 Evaluate side-chains 108 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 233 optimal weight: 0.0570 chunk 416 optimal weight: 0.0370 chunk 260 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 192 optimal weight: 0.0370 overall best weight: 3.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31986 Z= 0.264 Angle : 0.496 7.816 43740 Z= 0.269 Chirality : 0.044 0.192 5382 Planarity : 0.003 0.046 5940 Dihedral : 4.411 18.010 4854 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.65 % Allowed : 9.89 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.13), residues: 4338 helix: 0.18 (0.31), residues: 348 sheet: -0.47 (0.13), residues: 1500 loop : -0.49 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 722 HIS 0.003 0.002 HIS A 582 PHE 0.009 0.002 PHE D 295 TYR 0.013 0.002 TYR D 554 ARG 0.004 0.000 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 88 time to evaluate : 3.688 Fit side-chains REVERT: B 455 ASP cc_start: 0.8191 (m-30) cc_final: 0.7843 (t0) REVERT: B 578 ARG cc_start: 0.6698 (mmm160) cc_final: 0.6412 (mmm160) REVERT: B 626 GLN cc_start: 0.8868 (mt0) cc_final: 0.8279 (mm110) REVERT: D 455 ASP cc_start: 0.8058 (m-30) cc_final: 0.7689 (t0) REVERT: E 455 ASP cc_start: 0.8198 (m-30) cc_final: 0.7844 (t0) REVERT: E 578 ARG cc_start: 0.6711 (mmm160) cc_final: 0.6419 (mmm160) outliers start: 59 outliers final: 37 residues processed: 132 average time/residue: 0.3625 time to fit residues: 86.8833 Evaluate side-chains 124 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31986 Z= 0.329 Angle : 0.542 6.859 43740 Z= 0.294 Chirality : 0.045 0.178 5382 Planarity : 0.003 0.046 5940 Dihedral : 4.806 22.667 4854 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.90 % Allowed : 10.42 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.12), residues: 4338 helix: -0.19 (0.28), residues: 378 sheet: -0.73 (0.13), residues: 1536 loop : -0.62 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 722 HIS 0.003 0.002 HIS A 582 PHE 0.011 0.002 PHE A 295 TYR 0.014 0.002 TYR A 159 ARG 0.003 0.000 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 84 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8177 (m-30) cc_final: 0.7806 (t0) REVERT: B 626 GLN cc_start: 0.8871 (mt0) cc_final: 0.8276 (mm110) REVERT: D 455 ASP cc_start: 0.8175 (m-30) cc_final: 0.7838 (t0) REVERT: E 455 ASP cc_start: 0.8184 (m-30) cc_final: 0.7807 (t0) outliers start: 68 outliers final: 48 residues processed: 136 average time/residue: 0.3747 time to fit residues: 92.7953 Evaluate side-chains 128 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 80 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 614 LEU Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 6.9990 chunk 398 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 chunk 388 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 350 optimal weight: 8.9990 chunk 366 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31986 Z= 0.304 Angle : 0.526 6.943 43740 Z= 0.285 Chirality : 0.045 0.166 5382 Planarity : 0.003 0.045 5940 Dihedral : 4.757 21.847 4854 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.68 % Allowed : 10.98 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.10 (0.12), residues: 4338 helix: -0.21 (0.28), residues: 378 sheet: -0.79 (0.13), residues: 1536 loop : -0.69 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 722 HIS 0.003 0.002 HIS D 582 PHE 0.010 0.002 PHE D 295 TYR 0.014 0.002 TYR A 554 ARG 0.002 0.000 ARG D 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 79 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8152 (m-30) cc_final: 0.7788 (t0) REVERT: B 626 GLN cc_start: 0.8866 (mt0) cc_final: 0.8277 (mm110) REVERT: D 455 ASP cc_start: 0.8151 (m-30) cc_final: 0.7823 (t0) REVERT: E 455 ASP cc_start: 0.8161 (m-30) cc_final: 0.7794 (t0) outliers start: 60 outliers final: 49 residues processed: 126 average time/residue: 0.4029 time to fit residues: 90.5627 Evaluate side-chains 128 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 79 time to evaluate : 3.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 3.9990 chunk 410 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 285 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 396 optimal weight: 3.9990 chunk 342 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN F 508 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31986 Z= 0.316 Angle : 0.534 6.876 43740 Z= 0.291 Chirality : 0.045 0.164 5382 Planarity : 0.003 0.046 5940 Dihedral : 4.824 22.620 4854 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.57 % Allowed : 11.09 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.12), residues: 4338 helix: -0.19 (0.28), residues: 378 sheet: -0.84 (0.12), residues: 1536 loop : -0.76 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 722 HIS 0.003 0.002 HIS A 582 PHE 0.011 0.002 PHE A 295 TYR 0.014 0.002 TYR D 554 ARG 0.003 0.000 ARG F 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8676 Ramachandran restraints generated. 4338 Oldfield, 0 Emsley, 4338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 80 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 455 ASP cc_start: 0.8161 (m-30) cc_final: 0.7794 (t0) REVERT: B 626 GLN cc_start: 0.8865 (mt0) cc_final: 0.8278 (mm110) REVERT: D 455 ASP cc_start: 0.8163 (m-30) cc_final: 0.7834 (t0) REVERT: E 455 ASP cc_start: 0.8171 (m-30) cc_final: 0.7801 (t0) outliers start: 56 outliers final: 50 residues processed: 123 average time/residue: 0.3755 time to fit residues: 83.6611 Evaluate side-chains 128 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 78 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 681 MET Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 210 ASP Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 210 ASP Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 681 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.0470 chunk 365 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 316 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.072194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.057134 restraints weight = 136998.067| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.33 r_work: 0.3193 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31986 Z= 0.135 Angle : 0.461 7.749 43740 Z= 0.250 Chirality : 0.044 0.161 5382 Planarity : 0.003 0.047 5940 Dihedral : 4.222 17.225 4854 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.01 % Allowed : 11.71 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.13), residues: 4338 helix: -0.01 (0.29), residues: 384 sheet: -0.62 (0.12), residues: 1542 loop : -0.66 (0.13), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 722 HIS 0.003 0.002 HIS B 273 PHE 0.008 0.001 PHE A 514 TYR 0.014 0.001 TYR B 359 ARG 0.002 0.000 ARG F 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.41 seconds wall clock time: 94 minutes 40.03 seconds (5680.03 seconds total)