Starting phenix.real_space_refine on Sat Jul 4 16:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.cif Found real_map, /net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7om0_12982/07_2026/7om0_12982.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 66 5.16 5 C 14072 2.51 5 N 3676 2.21 5 O 4210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22042 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3636 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 426} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3644 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 427} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.31, per 1000 atoms: 0.20 Number of scatterers: 22042 At special positions: 0 Unit cell: (132.02, 118.9, 130.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 18 15.00 O 4210 8.00 N 3676 7.00 C 14072 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 717.4 milliseconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 45.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 361 Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.607A pdb=" N LEU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 418 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 486 through 502 removed outlier: 3.891A pdb=" N ASN A 502 " --> pdb=" O ASN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.515A pdb=" N VAL A 553 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 555 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.608A pdb=" N LEU A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.896A pdb=" N LYS A 644 " --> pdb=" O ASN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 712 through 719 removed outlier: 3.895A pdb=" N GLU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'B' and resid 317 through 339 Processing helix chain 'B' and resid 349 through 361 Processing helix chain 'B' and resid 387 through 399 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 486 through 502 removed outlier: 3.533A pdb=" N ASN B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 532 Processing helix chain 'B' and resid 550 through 557 removed outlier: 3.837A pdb=" N VAL B 553 " --> pdb=" O LYS B 550 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 556 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 557 " --> pdb=" O LEU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 583 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 640 through 646 removed outlier: 4.004A pdb=" N LYS B 644 " --> pdb=" O ASN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 650 through 664 Processing helix chain 'B' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'B' and resid 687 through 695 Processing helix chain 'B' and resid 706 through 718 removed outlier: 6.261A pdb=" N PHE B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR B 714 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 715 " --> pdb=" O TYR B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 737 Processing helix chain 'F' and resid 317 through 339 Processing helix chain 'F' and resid 349 through 361 Processing helix chain 'F' and resid 387 through 399 Processing helix chain 'F' and resid 403 through 418 Processing helix chain 'F' and resid 475 through 483 Processing helix chain 'F' and resid 486 through 502 Processing helix chain 'F' and resid 520 through 532 Processing helix chain 'F' and resid 550 through 555 removed outlier: 3.588A pdb=" N VAL F 553 " --> pdb=" O LYS F 550 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU F 555 " --> pdb=" O SER F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 583 Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.530A pdb=" N LEU F 622 " --> pdb=" O THR F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 646 removed outlier: 3.847A pdb=" N LYS F 644 " --> pdb=" O ASN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 647 through 649 No H-bonds generated for 'chain 'F' and resid 647 through 649' Processing helix chain 'F' and resid 650 through 664 Processing helix chain 'F' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'F' and resid 687 through 696 Processing helix chain 'F' and resid 706 through 719 removed outlier: 6.428A pdb=" N PHE F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR F 714 " --> pdb=" O VAL F 710 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS F 715 " --> pdb=" O TYR F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 728 through 737 Processing helix chain 'D' and resid 317 through 339 Processing helix chain 'D' and resid 349 through 361 Processing helix chain 'D' and resid 387 through 399 Processing helix chain 'D' and resid 403 through 418 Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'D' and resid 486 through 502 Processing helix chain 'D' and resid 520 through 532 Processing helix chain 'D' and resid 550 through 555 removed outlier: 3.578A pdb=" N VAL D 553 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 555 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 618 through 624 removed outlier: 3.502A pdb=" N LEU D 622 " --> pdb=" O THR D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 646 removed outlier: 3.903A pdb=" N LYS D 644 " --> pdb=" O ASN D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 650 through 664 Processing helix chain 'D' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'D' and resid 687 through 696 Processing helix chain 'D' and resid 706 through 719 removed outlier: 7.069A pdb=" N PHE D 713 " --> pdb=" O ILE D 709 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR D 714 " --> pdb=" O VAL D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 737 Processing helix chain 'E' and resid 317 through 339 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'E' and resid 387 through 399 removed outlier: 3.569A pdb=" N LEU E 398 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 418 Processing helix chain 'E' and resid 475 through 483 Processing helix chain 'E' and resid 486 through 502 removed outlier: 3.548A pdb=" N MET E 501 " --> pdb=" O ILE E 497 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN E 502 " --> pdb=" O ASN E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 532 Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.833A pdb=" N GLY E 556 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 557 " --> pdb=" O LEU E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 583 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.565A pdb=" N ARG E 624 " --> pdb=" O GLY E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 646 removed outlier: 4.031A pdb=" N LYS E 644 " --> pdb=" O ASN E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 649 No H-bonds generated for 'chain 'E' and resid 647 through 649' Processing helix chain 'E' and resid 650 through 664 Processing helix chain 'E' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'E' and resid 687 through 695 Processing helix chain 'E' and resid 706 through 712 Processing helix chain 'E' and resid 712 through 719 Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'C' and resid 317 through 339 Processing helix chain 'C' and resid 349 through 361 Processing helix chain 'C' and resid 387 through 399 removed outlier: 3.595A pdb=" N LEU C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 418 Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 486 through 502 removed outlier: 3.798A pdb=" N ASN C 502 " --> pdb=" O ASN C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 532 Processing helix chain 'C' and resid 550 through 555 removed outlier: 3.603A pdb=" N GLU C 555 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 583 Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.533A pdb=" N LEU C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 646 removed outlier: 3.893A pdb=" N LYS C 644 " --> pdb=" O ASN C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 664 Processing helix chain 'C' and resid 673 through 687 WARNING: missing atoms! Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 706 through 719 removed outlier: 6.117A pdb=" N PHE C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR C 714 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS C 715 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 716 " --> pdb=" O ALA C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.801A pdb=" N PHE C 731 " --> pdb=" O SER C 727 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431 Processing sheet with id=AA3, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA4, first strand: chain 'A' and resid 537 through 539 removed outlier: 5.809A pdb=" N ALA A 538 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP A 563 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 560 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER A 607 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 562 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 514 " --> pdb=" O VAL A 628 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA6, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.582A pdb=" N ALA A 598 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 363 through 365 Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 431 Processing sheet with id=AA9, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'B' and resid 537 through 538 removed outlier: 5.939A pdb=" N ALA B 538 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP B 563 " --> pdb=" O ALA B 538 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 564 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA B 510 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL B 628 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B 512 " --> pdb=" O VAL B 628 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 570 through 571 Processing sheet with id=AB3, first strand: chain 'B' and resid 586 through 588 Processing sheet with id=AB4, first strand: chain 'F' and resid 363 through 365 Processing sheet with id=AB5, first strand: chain 'F' and resid 429 through 431 Processing sheet with id=AB6, first strand: chain 'F' and resid 469 through 470 Processing sheet with id=AB7, first strand: chain 'F' and resid 537 through 539 removed outlier: 6.001A pdb=" N ALA F 538 " --> pdb=" O ILE F 561 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP F 563 " --> pdb=" O ALA F 538 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP F 564 " --> pdb=" O SER F 607 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA F 510 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL F 628 " --> pdb=" O ALA F 510 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE F 512 " --> pdb=" O VAL F 628 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 570 through 571 Processing sheet with id=AB9, first strand: chain 'F' and resid 586 through 588 Processing sheet with id=AC1, first strand: chain 'D' and resid 363 through 365 Processing sheet with id=AC2, first strand: chain 'D' and resid 429 through 431 Processing sheet with id=AC3, first strand: chain 'D' and resid 469 through 470 Processing sheet with id=AC4, first strand: chain 'D' and resid 537 through 539 removed outlier: 5.956A pdb=" N ALA D 538 " --> pdb=" O ILE D 561 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA D 510 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL D 628 " --> pdb=" O ALA D 510 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE D 512 " --> pdb=" O VAL D 628 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 570 through 571 Processing sheet with id=AC6, first strand: chain 'D' and resid 586 through 589 Processing sheet with id=AC7, first strand: chain 'E' and resid 363 through 364 Processing sheet with id=AC8, first strand: chain 'E' and resid 429 through 431 Processing sheet with id=AC9, first strand: chain 'E' and resid 469 through 470 Processing sheet with id=AD1, first strand: chain 'E' and resid 537 through 539 removed outlier: 5.795A pdb=" N ALA E 538 " --> pdb=" O ILE E 561 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP E 563 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP E 564 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 514 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 570 through 571 Processing sheet with id=AD3, first strand: chain 'E' and resid 586 through 588 removed outlier: 3.521A pdb=" N ALA E 598 " --> pdb=" O VAL E 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AD5, first strand: chain 'C' and resid 429 through 431 Processing sheet with id=AD6, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AD7, first strand: chain 'C' and resid 537 through 539 removed outlier: 5.837A pdb=" N ALA C 538 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP C 563 " --> pdb=" O ALA C 538 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 564 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA C 510 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 628 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE C 512 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 570 through 571 Processing sheet with id=AD9, first strand: chain 'C' and resid 586 through 589 removed outlier: 3.591A pdb=" N ALA C 598 " --> pdb=" O VAL C 586 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2586 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: 3.44 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6153 1.33 - 1.45: 3788 1.45 - 1.57: 12425 1.57 - 1.69: 31 1.69 - 1.81: 113 Bond restraints: 22510 Sorted by residual: bond pdb=" O3A ANP C1201 " pdb=" PB ANP C1201 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" O3A ANP B1201 " pdb=" PB ANP B1201 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP F1201 " pdb=" PB ANP F1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" O3A ANP A1201 " pdb=" PB ANP A1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" O3A ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.18e+01 ... (remaining 22505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 30284 3.56 - 7.13: 107 7.13 - 10.69: 12 10.69 - 14.25: 6 14.25 - 17.82: 6 Bond angle restraints: 30415 Sorted by residual: angle pdb=" PB ANP C1201 " pdb=" N3B ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sigma weight residual 126.95 109.13 17.82 3.00e+00 1.11e-01 3.53e+01 angle pdb=" PB ANP F1201 " pdb=" N3B ANP F1201 " pdb=" PG ANP F1201 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP A1201 " pdb=" N3B ANP A1201 " pdb=" PG ANP A1201 " ideal model delta sigma weight residual 126.95 109.30 17.65 3.00e+00 1.11e-01 3.46e+01 angle pdb=" PB ANP B1201 " pdb=" N3B ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sigma weight residual 126.95 109.32 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" PB ANP E1201 " pdb=" N3B ANP E1201 " pdb=" PG ANP E1201 " ideal model delta sigma weight residual 126.95 109.33 17.62 3.00e+00 1.11e-01 3.45e+01 ... (remaining 30410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 13231 33.19 - 66.38: 214 66.38 - 99.57: 14 99.57 - 132.75: 0 132.75 - 165.94: 6 Dihedral angle restraints: 13465 sinusoidal: 5644 harmonic: 7821 Sorted by residual: dihedral pdb=" O1B ANP C1201 " pdb=" N3B ANP C1201 " pdb=" PB ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sinusoidal sigma weight residual 35.15 -130.79 165.94 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B ANP B1201 " pdb=" N3B ANP B1201 " pdb=" PB ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sinusoidal sigma weight residual 35.15 -129.46 164.61 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O1B ANP E1201 " pdb=" N3B ANP E1201 " pdb=" PB ANP E1201 " pdb=" PG ANP E1201 " ideal model delta sinusoidal sigma weight residual 35.15 -129.25 164.40 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2727 0.056 - 0.111: 470 0.111 - 0.167: 57 0.167 - 0.222: 2 0.222 - 0.278: 7 Chirality restraints: 3263 Sorted by residual: chirality pdb=" C3' ANP B1201 " pdb=" C2' ANP B1201 " pdb=" C4' ANP B1201 " pdb=" O3' ANP B1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP C1201 " pdb=" C2' ANP C1201 " pdb=" C4' ANP C1201 " pdb=" O3' ANP C1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ANP A1201 " pdb=" C2' ANP A1201 " pdb=" C4' ANP A1201 " pdb=" O3' ANP A1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3260 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 349 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO D 350 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 350 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 350 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 448 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 449 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 448 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO E 449 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO E 449 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 449 " 0.018 5.00e-02 4.00e+02 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2104 2.75 - 3.29: 23036 3.29 - 3.82: 36442 3.82 - 4.36: 44988 4.36 - 4.90: 74127 Nonbonded interactions: 180697 Sorted by model distance: nonbonded pdb=" OG SER A 574 " pdb=" OD2 ASP A 616 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLU E 680 " pdb=" OH TYR E 690 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 574 " pdb=" OD2 ASP C 616 " model vdw 2.223 3.040 nonbonded pdb=" OG SER F 574 " pdb=" OD2 ASP F 616 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU D 547 " pdb=" NZ LYS D 550 " model vdw 2.246 3.120 ... (remaining 180692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 316 through 750 or resid 754 through 1201)) selection = (chain 'B' and (resid 316 through 750 or resid 754 through 1201)) selection = (chain 'C' and (resid 316 through 750 or resid 754 through 1201)) selection = chain 'D' selection = (chain 'E' and (resid 316 through 750 or resid 754 through 1201)) selection = (chain 'F' and (resid 316 through 750 or resid 754 through 1201)) } 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 18.100 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 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 : 0.004 0.145 22510 Z= 0.242 Angle : 0.633 17.815 30415 Z= 0.324 Chirality : 0.043 0.278 3263 Planarity : 0.003 0.033 3898 Dihedral : 13.266 165.942 8415 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.16), residues: 2597 helix: 2.35 (0.16), residues: 1037 sheet: 0.21 (0.33), residues: 250 loop : -0.28 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 597 TYR 0.019 0.001 TYR D 711 PHE 0.021 0.001 PHE B 713 TRP 0.008 0.001 TRP C 335 HIS 0.006 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.24 (22510) covalent geometry : angle 0.63315 / 0.32 (30415) hydrogen bonds : bond 0.17284 / 11.97 ( 900) hydrogen bonds : angle 6.13486 / 4.31 ( 2586) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.959 Fit side-chains REVERT: A 708 TYR cc_start: 0.8627 (p90) cc_final: 0.8240 (p90) REVERT: A 732 TYR cc_start: 0.7985 (t80) cc_final: 0.7683 (t80) REVERT: B 331 MET cc_start: 0.8724 (mtp) cc_final: 0.8450 (mtp) REVERT: B 737 HIS cc_start: 0.8696 (t70) cc_final: 0.8159 (t70) REVERT: F 690 TYR cc_start: 0.9176 (t80) cc_final: 0.8460 (t80) REVERT: F 737 HIS cc_start: 0.8415 (t70) cc_final: 0.7875 (t70) REVERT: D 737 HIS cc_start: 0.8420 (t70) cc_final: 0.7864 (t70) REVERT: C 331 MET cc_start: 0.8938 (mtp) cc_final: 0.8730 (mtp) REVERT: C 690 TYR cc_start: 0.9119 (t80) cc_final: 0.8539 (t80) REVERT: C 737 HIS cc_start: 0.8463 (t70) cc_final: 0.7995 (t70) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1425 time to fit residues: 22.4848 Evaluate side-chains 77 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 595 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.082639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053908 restraints weight = 80791.569| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.50 r_work: 0.2822 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22510 Z= 0.236 Angle : 0.512 5.229 30415 Z= 0.282 Chirality : 0.043 0.181 3263 Planarity : 0.004 0.051 3898 Dihedral : 8.590 160.048 2893 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.37 % Allowed : 4.12 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 2597 helix: 2.23 (0.16), residues: 1094 sheet: 0.30 (0.36), residues: 225 loop : -0.21 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 439 TYR 0.013 0.001 TYR F 717 PHE 0.013 0.001 PHE C 735 TRP 0.006 0.001 TRP C 335 HIS 0.007 0.001 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (22510) covalent geometry : angle 0.51248 / 0.28 (30415) hydrogen bonds : bond 0.04653 / 3.17 ( 900) hydrogen bonds : angle 5.08832 / 3.54 ( 2586) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.846 Fit side-chains REVERT: A 708 TYR cc_start: 0.8512 (p90) cc_final: 0.8279 (p90) REVERT: A 737 HIS cc_start: 0.8415 (t70) cc_final: 0.7987 (m90) REVERT: B 737 HIS cc_start: 0.8594 (t70) cc_final: 0.7797 (t70) REVERT: F 690 TYR cc_start: 0.8928 (t80) cc_final: 0.8182 (t80) REVERT: F 737 HIS cc_start: 0.8428 (t70) cc_final: 0.7773 (t70) REVERT: D 737 HIS cc_start: 0.8524 (t70) cc_final: 0.7896 (t70) REVERT: E 737 HIS cc_start: 0.8588 (t70) cc_final: 0.7950 (m90) REVERT: C 690 TYR cc_start: 0.9048 (t80) cc_final: 0.8301 (t80) REVERT: C 737 HIS cc_start: 0.8647 (t70) cc_final: 0.8054 (t70) outliers start: 9 outliers final: 1 residues processed: 82 average time/residue: 0.1277 time to fit residues: 18.1680 Evaluate side-chains 80 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 81 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 215 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN E 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.083959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056426 restraints weight = 82520.262| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.47 r_work: 0.2870 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22510 Z= 0.135 Angle : 0.442 6.729 30415 Z= 0.245 Chirality : 0.041 0.174 3263 Planarity : 0.003 0.048 3898 Dihedral : 8.493 159.107 2893 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.91 % Allowed : 5.93 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.16), residues: 2597 helix: 2.33 (0.16), residues: 1094 sheet: 0.23 (0.36), residues: 220 loop : -0.23 (0.16), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 507 TYR 0.025 0.001 TYR D 711 PHE 0.012 0.001 PHE C 735 TRP 0.004 0.001 TRP B 478 HIS 0.004 0.001 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (22510) covalent geometry : angle 0.44157 / 0.25 (30415) hydrogen bonds : bond 0.03901 / 2.66 ( 900) hydrogen bonds : angle 4.71718 / 3.27 ( 2586) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.039 Fit side-chains REVERT: A 708 TYR cc_start: 0.8520 (p90) cc_final: 0.8265 (p90) REVERT: A 737 HIS cc_start: 0.8455 (t70) cc_final: 0.7996 (m90) REVERT: B 737 HIS cc_start: 0.8608 (t70) cc_final: 0.7796 (t70) REVERT: F 690 TYR cc_start: 0.8962 (t80) cc_final: 0.8153 (t80) REVERT: F 737 HIS cc_start: 0.8445 (t70) cc_final: 0.7757 (t70) REVERT: D 737 HIS cc_start: 0.8507 (t70) cc_final: 0.7838 (t70) REVERT: E 737 HIS cc_start: 0.8515 (t70) cc_final: 0.7893 (m90) REVERT: C 690 TYR cc_start: 0.9036 (t80) cc_final: 0.8273 (t80) REVERT: C 737 HIS cc_start: 0.8610 (t70) cc_final: 0.8019 (t70) outliers start: 22 outliers final: 8 residues processed: 87 average time/residue: 0.1270 time to fit residues: 19.5836 Evaluate side-chains 87 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 731 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 0.0980 chunk 147 optimal weight: 0.0070 chunk 252 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.084173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056612 restraints weight = 82850.497| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.48 r_work: 0.2879 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22510 Z= 0.120 Angle : 0.432 8.360 30415 Z= 0.239 Chirality : 0.041 0.166 3263 Planarity : 0.003 0.049 3898 Dihedral : 8.407 158.685 2893 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.74 % Allowed : 7.00 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2597 helix: 2.39 (0.16), residues: 1099 sheet: 0.21 (0.36), residues: 220 loop : -0.24 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.024 0.001 TYR D 711 PHE 0.006 0.001 PHE A 363 TRP 0.003 0.001 TRP E 478 HIS 0.004 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22510) covalent geometry : angle 0.43226 / 0.24 (30415) hydrogen bonds : bond 0.03530 / 2.39 ( 900) hydrogen bonds : angle 4.54018 / 3.14 ( 2586) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.588 Fit side-chains REVERT: A 708 TYR cc_start: 0.8489 (p90) cc_final: 0.8222 (p90) REVERT: A 737 HIS cc_start: 0.8504 (t70) cc_final: 0.8051 (m90) REVERT: B 737 HIS cc_start: 0.8631 (t70) cc_final: 0.7831 (t70) REVERT: F 690 TYR cc_start: 0.8958 (t80) cc_final: 0.8149 (t80) REVERT: F 737 HIS cc_start: 0.8482 (t70) cc_final: 0.7853 (t70) REVERT: D 737 HIS cc_start: 0.8506 (t70) cc_final: 0.7873 (t70) REVERT: E 737 HIS cc_start: 0.8526 (t70) cc_final: 0.7884 (m90) REVERT: C 690 TYR cc_start: 0.9050 (t80) cc_final: 0.8277 (t80) REVERT: C 737 HIS cc_start: 0.8656 (t70) cc_final: 0.8077 (t70) outliers start: 18 outliers final: 7 residues processed: 83 average time/residue: 0.1195 time to fit residues: 17.3455 Evaluate side-chains 85 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 167 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 129 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.084394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056619 restraints weight = 83697.219| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.53 r_work: 0.2880 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22510 Z= 0.113 Angle : 0.428 7.472 30415 Z= 0.236 Chirality : 0.041 0.168 3263 Planarity : 0.003 0.046 3898 Dihedral : 8.330 158.974 2891 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.49 % Allowed : 8.19 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.16), residues: 2597 helix: 2.46 (0.16), residues: 1099 sheet: 0.24 (0.37), residues: 220 loop : -0.25 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.021 0.001 TYR F 717 PHE 0.006 0.001 PHE A 363 TRP 0.003 0.001 TRP E 335 HIS 0.003 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22510) covalent geometry : angle 0.42822 / 0.24 (30415) hydrogen bonds : bond 0.03340 / 2.26 ( 900) hydrogen bonds : angle 4.43776 / 3.08 ( 2586) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.952 Fit side-chains REVERT: A 708 TYR cc_start: 0.8425 (p90) cc_final: 0.8176 (p90) REVERT: A 737 HIS cc_start: 0.8518 (t70) cc_final: 0.8068 (m90) REVERT: B 737 HIS cc_start: 0.8631 (t70) cc_final: 0.7834 (t70) REVERT: F 690 TYR cc_start: 0.8949 (t80) cc_final: 0.8142 (t80) REVERT: F 737 HIS cc_start: 0.8470 (t70) cc_final: 0.7851 (t70) REVERT: D 737 HIS cc_start: 0.8523 (t70) cc_final: 0.7881 (t70) REVERT: E 737 HIS cc_start: 0.8527 (t70) cc_final: 0.7898 (m90) REVERT: C 690 TYR cc_start: 0.9061 (t80) cc_final: 0.8294 (t80) REVERT: C 737 HIS cc_start: 0.8650 (t70) cc_final: 0.8052 (t70) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1340 time to fit residues: 19.4011 Evaluate side-chains 86 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 731 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 62 optimal weight: 10.0000 chunk 181 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 203 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055517 restraints weight = 84967.904| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.69 r_work: 0.2849 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22510 Z= 0.146 Angle : 0.442 7.838 30415 Z= 0.243 Chirality : 0.041 0.158 3263 Planarity : 0.003 0.046 3898 Dihedral : 8.301 158.815 2891 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.91 % Allowed : 8.32 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2597 helix: 2.45 (0.16), residues: 1100 sheet: 0.26 (0.37), residues: 220 loop : -0.29 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.032 0.001 TYR B 717 PHE 0.007 0.001 PHE F 682 TRP 0.003 0.001 TRP E 335 HIS 0.003 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (22510) covalent geometry : angle 0.44214 / 0.24 (30415) hydrogen bonds : bond 0.03431 / 2.32 ( 900) hydrogen bonds : angle 4.45784 / 3.10 ( 2586) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.795 Fit side-chains REVERT: A 708 TYR cc_start: 0.8410 (p90) cc_final: 0.8209 (p90) REVERT: A 737 HIS cc_start: 0.8465 (t70) cc_final: 0.8026 (m90) REVERT: B 737 HIS cc_start: 0.8507 (t70) cc_final: 0.7683 (t70) REVERT: F 690 TYR cc_start: 0.8849 (t80) cc_final: 0.8042 (t80) REVERT: F 737 HIS cc_start: 0.8361 (t70) cc_final: 0.7638 (t70) REVERT: D 737 HIS cc_start: 0.8458 (t70) cc_final: 0.7765 (t70) REVERT: E 713 PHE cc_start: 0.9280 (t80) cc_final: 0.9050 (t80) REVERT: E 737 HIS cc_start: 0.8527 (t70) cc_final: 0.7948 (m90) REVERT: C 690 TYR cc_start: 0.9000 (t80) cc_final: 0.8242 (t80) REVERT: C 737 HIS cc_start: 0.8565 (t70) cc_final: 0.7891 (t70) outliers start: 22 outliers final: 9 residues processed: 91 average time/residue: 0.1226 time to fit residues: 19.6311 Evaluate side-chains 88 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 689 VAL Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 138 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 244 optimal weight: 0.0030 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.084970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.055971 restraints weight = 84317.684| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.65 r_work: 0.2863 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22510 Z= 0.126 Angle : 0.437 9.068 30415 Z= 0.241 Chirality : 0.041 0.197 3263 Planarity : 0.003 0.045 3898 Dihedral : 8.227 157.888 2891 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.78 % Allowed : 8.60 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2597 helix: 2.47 (0.16), residues: 1100 sheet: 0.28 (0.37), residues: 220 loop : -0.27 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.031 0.001 TYR B 717 PHE 0.005 0.001 PHE A 363 TRP 0.004 0.001 TRP A 473 HIS 0.003 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (22510) covalent geometry : angle 0.43713 / 0.24 (30415) hydrogen bonds : bond 0.03312 / 2.23 ( 900) hydrogen bonds : angle 4.40898 / 3.07 ( 2586) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8441 (p90) cc_final: 0.8220 (p90) REVERT: A 737 HIS cc_start: 0.8476 (t70) cc_final: 0.8030 (m90) REVERT: B 737 HIS cc_start: 0.8531 (t70) cc_final: 0.7699 (t70) REVERT: F 690 TYR cc_start: 0.8877 (t80) cc_final: 0.8068 (t80) REVERT: F 737 HIS cc_start: 0.8367 (t70) cc_final: 0.7648 (t70) REVERT: D 737 HIS cc_start: 0.8469 (t70) cc_final: 0.7774 (t70) REVERT: E 737 HIS cc_start: 0.8530 (t70) cc_final: 0.7941 (m90) REVERT: C 690 TYR cc_start: 0.9004 (t80) cc_final: 0.8225 (t80) REVERT: C 737 HIS cc_start: 0.8565 (t70) cc_final: 0.7892 (t70) outliers start: 19 outliers final: 11 residues processed: 90 average time/residue: 0.1186 time to fit residues: 18.7832 Evaluate side-chains 89 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain F residue 689 VAL Chi-restraints excluded: chain F residue 731 PHE Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 234 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 chunk 82 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.085003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.056294 restraints weight = 83163.852| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.62 r_work: 0.2872 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22510 Z= 0.109 Angle : 0.432 9.965 30415 Z= 0.238 Chirality : 0.041 0.188 3263 Planarity : 0.003 0.046 3898 Dihedral : 8.183 158.337 2891 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.62 % Allowed : 8.89 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2597 helix: 2.46 (0.16), residues: 1106 sheet: 0.31 (0.37), residues: 220 loop : -0.25 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.030 0.001 TYR D 711 PHE 0.006 0.001 PHE A 363 TRP 0.003 0.000 TRP A 473 HIS 0.003 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (22510) covalent geometry : angle 0.43202 / 0.24 (30415) hydrogen bonds : bond 0.03181 / 2.15 ( 900) hydrogen bonds : angle 4.36106 / 3.03 ( 2586) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8428 (p90) cc_final: 0.8162 (p90) REVERT: A 737 HIS cc_start: 0.8474 (t70) cc_final: 0.8115 (m90) REVERT: B 737 HIS cc_start: 0.8606 (t70) cc_final: 0.7807 (t70) REVERT: F 690 TYR cc_start: 0.8933 (t80) cc_final: 0.8066 (t80) REVERT: F 737 HIS cc_start: 0.8413 (t70) cc_final: 0.7782 (t70) REVERT: D 737 HIS cc_start: 0.8502 (t70) cc_final: 0.7861 (t70) REVERT: E 333 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8913 (mm-30) REVERT: E 737 HIS cc_start: 0.8541 (t70) cc_final: 0.7939 (m90) REVERT: C 690 TYR cc_start: 0.9054 (t80) cc_final: 0.8414 (t80) REVERT: C 737 HIS cc_start: 0.8616 (t70) cc_final: 0.8195 (m90) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.1318 time to fit residues: 19.7998 Evaluate side-chains 88 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain F residue 689 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 226 optimal weight: 1.9990 chunk 87 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 216 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.083778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054575 restraints weight = 84098.615| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.69 r_work: 0.2829 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22510 Z= 0.184 Angle : 0.474 10.476 30415 Z= 0.259 Chirality : 0.042 0.234 3263 Planarity : 0.003 0.045 3898 Dihedral : 8.200 157.641 2891 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.54 % Allowed : 9.18 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2597 helix: 2.36 (0.16), residues: 1106 sheet: 0.29 (0.37), residues: 220 loop : -0.28 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.027 0.001 TYR D 711 PHE 0.008 0.001 PHE F 682 TRP 0.004 0.001 TRP E 494 HIS 0.002 0.001 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (22510) covalent geometry : angle 0.47436 / 0.26 (30415) hydrogen bonds : bond 0.03574 / 2.42 ( 900) hydrogen bonds : angle 4.52722 / 3.15 ( 2586) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8465 (p90) cc_final: 0.8203 (p90) REVERT: A 737 HIS cc_start: 0.8476 (t70) cc_final: 0.8079 (m90) REVERT: B 737 HIS cc_start: 0.8594 (t70) cc_final: 0.7799 (t70) REVERT: F 690 TYR cc_start: 0.8926 (t80) cc_final: 0.8049 (t80) REVERT: F 737 HIS cc_start: 0.8396 (t70) cc_final: 0.7707 (t70) REVERT: D 737 HIS cc_start: 0.8475 (t70) cc_final: 0.7820 (t70) REVERT: E 690 TYR cc_start: 0.8846 (t80) cc_final: 0.8289 (t80) REVERT: E 713 PHE cc_start: 0.9231 (t80) cc_final: 0.8947 (t80) REVERT: E 737 HIS cc_start: 0.8573 (t70) cc_final: 0.7957 (m90) REVERT: C 690 TYR cc_start: 0.9067 (t80) cc_final: 0.8454 (t80) REVERT: C 737 HIS cc_start: 0.8561 (t70) cc_final: 0.8142 (m90) outliers start: 13 outliers final: 11 residues processed: 86 average time/residue: 0.1232 time to fit residues: 18.2240 Evaluate side-chains 89 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain A residue 731 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain F residue 689 VAL Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 231 optimal weight: 0.2980 chunk 131 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.084690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056110 restraints weight = 83355.718| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.62 r_work: 0.2878 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22510 Z= 0.100 Angle : 0.435 10.697 30415 Z= 0.238 Chirality : 0.041 0.227 3263 Planarity : 0.003 0.051 3898 Dihedral : 8.104 157.230 2891 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.54 % Allowed : 9.39 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2597 helix: 2.46 (0.16), residues: 1106 sheet: 0.26 (0.37), residues: 220 loop : -0.25 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.029 0.001 TYR D 711 PHE 0.005 0.001 PHE A 363 TRP 0.003 0.000 TRP A 473 HIS 0.003 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (22510) covalent geometry : angle 0.43507 / 0.24 (30415) hydrogen bonds : bond 0.03162 / 2.14 ( 900) hydrogen bonds : angle 4.34176 / 3.02 ( 2586) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 708 TYR cc_start: 0.8420 (p90) cc_final: 0.8197 (p90) REVERT: A 737 HIS cc_start: 0.8460 (t70) cc_final: 0.8078 (m90) REVERT: B 737 HIS cc_start: 0.8560 (t70) cc_final: 0.7914 (t70) REVERT: F 690 TYR cc_start: 0.8900 (t80) cc_final: 0.8036 (t80) REVERT: F 737 HIS cc_start: 0.8395 (t70) cc_final: 0.7695 (t70) REVERT: D 737 HIS cc_start: 0.8474 (t70) cc_final: 0.7798 (t70) REVERT: E 333 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8912 (mm-30) REVERT: E 737 HIS cc_start: 0.8532 (t70) cc_final: 0.7944 (m90) REVERT: C 690 TYR cc_start: 0.9021 (t80) cc_final: 0.8367 (t80) REVERT: C 737 HIS cc_start: 0.8574 (t70) cc_final: 0.8125 (m90) outliers start: 13 outliers final: 10 residues processed: 86 average time/residue: 0.1232 time to fit residues: 18.4882 Evaluate side-chains 89 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 645 GLU Chi-restraints excluded: chain F residue 689 VAL Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 689 VAL Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 689 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 5 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 157 optimal weight: 0.0870 chunk 179 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 ASN E 471 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.085513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.056680 restraints weight = 84226.806| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.69 r_work: 0.2889 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22510 Z= 0.093 Angle : 0.432 10.925 30415 Z= 0.238 Chirality : 0.041 0.227 3263 Planarity : 0.003 0.053 3898 Dihedral : 8.088 158.878 2891 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.58 % Allowed : 9.51 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.17), residues: 2597 helix: 2.53 (0.16), residues: 1106 sheet: 0.27 (0.37), residues: 220 loop : -0.28 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 703 TYR 0.030 0.001 TYR D 711 PHE 0.005 0.001 PHE A 363 TRP 0.003 0.000 TRP E 743 HIS 0.003 0.000 HIS E 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (22510) covalent geometry : angle 0.43189 / 0.24 (30415) hydrogen bonds : bond 0.02999 / 2.02 ( 900) hydrogen bonds : angle 4.26353 / 2.97 ( 2586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5771.20 seconds wall clock time: 99 minutes 36.70 seconds (5976.70 seconds total)