Starting phenix.real_space_refine on Mon May 19 12:32:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b64_44245/05_2025/9b64_44245.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b64_44245/05_2025/9b64_44245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b64_44245/05_2025/9b64_44245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b64_44245/05_2025/9b64_44245.map" model { file = "/net/cci-nas-00/data/ceres_data/9b64_44245/05_2025/9b64_44245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b64_44245/05_2025/9b64_44245.cif" } resolution = 3.56 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 12029 2.51 5 N 2984 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18493 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 404, 3140 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 3190 Chain: "B" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 408, 3166 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 3222 Chain: "A" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3133 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 391} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 3180 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 408, 3164 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3215 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS C 435 " occ=0.25 ... (18 atoms not shown) pdb=" NE2BHIS C 435 " occ=0.75 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.57 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.43 Time building chain proxies: 15.28, per 1000 atoms: 0.83 Number of scatterers: 18493 At special positions: 0 Unit cell: (116.44, 110.7, 146.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3352 8.00 N 2984 7.00 C 12029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 3.9 seconds 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4366 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 61.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.552A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.783A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.953A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 162 " --> pdb=" O SER H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 removed outlier: 3.642A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.875A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.883A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 removed outlier: 3.665A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.907A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.825A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.779A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.800A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.870A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 489 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.853A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 635 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.800A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 removed outlier: 3.534A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.682A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.890A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.767A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.550A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.844A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 removed outlier: 3.558A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.772A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 489 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.813A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 635 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.749A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.784A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 29 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 126 removed outlier: 3.560A pdb=" N ILE G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.701A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.720A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AA4, first strand: chain 'C' and resid 406 through 408 Processing sheet with id=AA5, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AA6, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.564A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.820A pdb=" N LEU C 703 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.285A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 439 through 444 removed outlier: 6.285A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA B 477 " --> pdb=" O ASP B 733 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP B 733 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 479 " --> pdb=" O GLY B 731 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLY B 731 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 removed outlier: 3.520A pdb=" N GLU B 422 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.543A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 440 through 444 removed outlier: 3.699A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.661A pdb=" N ALA A 452 " --> pdb=" O ASN A 461 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AB7, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.665A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 646 through 648 removed outlier: 8.183A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 440 through 444 removed outlier: 6.437A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 490 through 491 Processing sheet with id=AC3, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.608A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 646 through 648 removed outlier: 8.392A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC6, first strand: chain 'G' and resid 78 through 79 1216 hydrogen bonds defined for protein. 3526 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: 6.21 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5691 1.34 - 1.46: 4848 1.46 - 1.58: 8161 1.58 - 1.70: 1 1.70 - 1.82: 208 Bond restraints: 18909 Sorted by residual: bond pdb=" CB PRO C 745 " pdb=" CG PRO C 745 " ideal model delta sigma weight residual 1.492 1.591 -0.099 5.00e-02 4.00e+02 3.88e+00 bond pdb=" CG LEU B 751 " pdb=" CD2 LEU B 751 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.42e+00 bond pdb=" CB GLU D 705 " pdb=" CG GLU D 705 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CB GLU C 644 " pdb=" CG GLU C 644 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB PRO C 737 " pdb=" CG PRO C 737 " ideal model delta sigma weight residual 1.492 1.546 -0.054 5.00e-02 4.00e+02 1.17e+00 ... (remaining 18904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 25303 2.58 - 5.15: 225 5.15 - 7.73: 21 7.73 - 10.31: 13 10.31 - 12.88: 3 Bond angle restraints: 25565 Sorted by residual: angle pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" CD PRO C 745 " ideal model delta sigma weight residual 112.00 104.26 7.74 1.40e+00 5.10e-01 3.05e+01 angle pdb=" C LYS C 765 " pdb=" N TRP C 766 " pdb=" CA TRP C 766 " ideal model delta sigma weight residual 122.49 114.45 8.04 1.55e+00 4.16e-01 2.69e+01 angle pdb=" CG ARG F 99 " pdb=" CD ARG F 99 " pdb=" NE ARG F 99 " ideal model delta sigma weight residual 112.00 121.95 -9.95 2.20e+00 2.07e-01 2.04e+01 angle pdb=" CB MET C 408 " pdb=" CG MET C 408 " pdb=" SD MET C 408 " ideal model delta sigma weight residual 112.70 125.58 -12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA GLN E 207 " pdb=" CB GLN E 207 " pdb=" CG GLN E 207 " ideal model delta sigma weight residual 114.10 122.17 -8.07 2.00e+00 2.50e-01 1.63e+01 ... (remaining 25560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9443 17.86 - 35.72: 1281 35.72 - 53.57: 285 53.57 - 71.43: 33 71.43 - 89.29: 25 Dihedral angle restraints: 11067 sinusoidal: 4227 harmonic: 6840 Sorted by residual: dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 165.14 -72.14 1 1.00e+01 1.00e-02 6.66e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 157.65 -64.65 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS B 718 " pdb=" SG CYS B 718 " pdb=" SG CYS B 773 " pdb=" CB CYS B 773 " ideal model delta sinusoidal sigma weight residual 93.00 151.50 -58.50 1 1.00e+01 1.00e-02 4.58e+01 ... (remaining 11064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1964 0.036 - 0.072: 693 0.072 - 0.107: 177 0.107 - 0.143: 38 0.143 - 0.179: 5 Chirality restraints: 2877 Sorted by residual: chirality pdb=" CA PRO C 745 " pdb=" N PRO C 745 " pdb=" C PRO C 745 " pdb=" CB PRO C 745 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CB ILE A 812 " pdb=" CA ILE A 812 " pdb=" CG1 ILE A 812 " pdb=" CG2 ILE A 812 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA TRP C 766 " pdb=" N TRP C 766 " pdb=" C TRP C 766 " pdb=" CB TRP C 766 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 2874 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 766 " -0.034 2.00e-02 2.50e+03 3.38e-02 2.86e+01 pdb=" CG TRP C 766 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP C 766 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP C 766 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 766 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 766 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 766 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 766 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 766 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 766 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 671 " -0.039 2.00e-02 2.50e+03 3.14e-02 2.47e+01 pdb=" CG TRP B 671 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP B 671 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 671 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 671 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 671 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 671 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 671 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 671 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 671 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 403 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 404 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 404 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 404 " 0.050 5.00e-02 4.00e+02 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1628 2.74 - 3.28: 19039 3.28 - 3.82: 32205 3.82 - 4.36: 35342 4.36 - 4.90: 62298 Nonbonded interactions: 150512 Sorted by model distance: nonbonded pdb=" N LEU G 3 " pdb=" OE1 GLN G 9 " model vdw 2.201 3.120 nonbonded pdb=" O VAL C 681 " pdb=" OH TYR C 700 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 635 " pdb=" OD1 ASP B 638 " model vdw 2.242 3.040 nonbonded pdb=" OE1 GLU A 657 " pdb=" NH2 ARG A 660 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN B 642 " pdb=" O ILE B 645 " model vdw 2.261 3.120 ... (remaining 150507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 575 or (resid 576 and (name N or name CA or name C or name \ O or name CB )) or resid 577 through 622 or resid 624 through 626 or (resid 627 \ and (name N or name CA or name C or name O or name CB )) or resid 628 through 7 \ 63 or resid 765 through 812 or (resid 813 and (name N or name CA or name C or na \ me O or name CB )) or resid 814 through 818 or (resid 819 through 820 and (name \ N or name CA or name C or name O or name CB )) or resid 821 through 825)) selection = (chain 'B' and (resid 393 through 409 or (resid 410 and (name N or name CA or na \ me C or name O or name CB )) or resid 411 through 434 or resid 436 through 438 o \ r (resid 439 and (name N or name CA or name C or name O or name CB or name CG )) \ or resid 440 through 506 or (resid 511 and (name N or name CA or name C or name \ O or name CB )) or resid 512 through 575 or (resid 576 and (name N or name CA o \ r name C or name O or name CB )) or resid 577 through 593 or (resid 594 and (nam \ e N or name CA or name C or name O or name CB )) or resid 595 through 622 or res \ id 624 through 626 or (resid 627 and (name N or name CA or name C or name O or n \ ame CB )) or resid 628 through 763 or resid 765 through 773 or (resid 784 and (n \ ame N or name CA or name C or name O or name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 393 through 434 or resid 436 through 593 or (resid 594 and \ (name N or name CA or name C or name O or name CB )) or resid 595 through 622 o \ r resid 624 through 626 or (resid 627 and (name N or name CA or name C or name O \ or name CB )) or resid 628 through 666 or (resid 667 and (name N or name CA or \ name C or name O or name CB )) or resid 668 through 763 or resid 765 through 812 \ or (resid 813 and (name N or name CA or name C or name O or name CB )) or resid \ 814 through 818 or (resid 819 through 820 and (name N or name CA or name C or n \ ame O or name CB )) or resid 821 through 825)) selection = (chain 'D' and (resid 393 through 434 or resid 436 through 506 or (resid 511 and \ (name N or name CA or name C or name O or name CB )) or resid 512 through 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 622 or resid 624 through 666 or (resid 667 and (name \ N or name CA or name C or name O or name CB )) or resid 668 through 763 or resid \ 765 through 773 or (resid 784 and (name N or name CA or name C or name O or nam \ e CB )) or resid 785 through 825)) } ncs_group { reference = (chain 'E' and resid 5 through 214) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214)) selection = (chain 'G' and resid 5 through 214) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 48.520 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.003 0.099 18921 Z= 0.136 Angle : 0.642 12.884 25589 Z= 0.337 Chirality : 0.039 0.179 2877 Planarity : 0.005 0.102 3155 Dihedral : 16.807 89.291 6665 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.15 % Allowed : 27.72 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.70 (0.18), residues: 2337 helix: 2.44 (0.14), residues: 1393 sheet: -0.74 (0.37), residues: 192 loop : -0.91 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.002 TRP C 766 HIS 0.007 0.001 HIS H 205 PHE 0.015 0.001 PHE D 658 TYR 0.019 0.001 TYR E 156 ARG 0.010 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.12805 ( 1211) hydrogen bonds : angle 4.92658 ( 3526) SS BOND : bond 0.00430 ( 12) SS BOND : angle 1.64815 ( 24) covalent geometry : bond 0.00299 (18909) covalent geometry : angle 0.64008 (25565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 346 time to evaluate : 2.255 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8596 (mp) REVERT: F 117 MET cc_start: 0.7842 (mmt) cc_final: 0.7639 (mmm) REVERT: F 178 TRP cc_start: 0.7586 (p-90) cc_final: 0.4641 (m100) REVERT: F 204 ARG cc_start: 0.6746 (ptm160) cc_final: 0.6543 (ptm160) REVERT: C 641 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7445 (mttt) REVERT: A 769 ASP cc_start: 0.7559 (m-30) cc_final: 0.7324 (t0) REVERT: D 816 TYR cc_start: 0.7431 (t80) cc_final: 0.7179 (t80) REVERT: E 5 ASP cc_start: 0.5721 (m-30) cc_final: 0.5263 (m-30) REVERT: E 78 LYS cc_start: 0.7427 (ptmt) cc_final: 0.6807 (pttt) outliers start: 3 outliers final: 2 residues processed: 348 average time/residue: 0.3085 time to fit residues: 161.4496 Evaluate side-chains 330 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain G residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 118 optimal weight: 0.0170 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 0.0670 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 0.7980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN F 149 ASN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN G 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.136421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096379 restraints weight = 89947.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100871 restraints weight = 32567.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.103689 restraints weight = 18782.880| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18921 Z= 0.107 Angle : 0.521 10.054 25589 Z= 0.268 Chirality : 0.039 0.179 2877 Planarity : 0.004 0.083 3155 Dihedral : 3.748 57.443 2568 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.31 % Allowed : 25.00 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2337 helix: 2.87 (0.14), residues: 1403 sheet: -0.51 (0.38), residues: 180 loop : -0.86 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP C 766 HIS 0.006 0.001 HIS E 82 PHE 0.012 0.001 PHE C 814 TYR 0.014 0.001 TYR B 673 ARG 0.008 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 1211) hydrogen bonds : angle 3.70331 ( 3526) SS BOND : bond 0.00294 ( 12) SS BOND : angle 0.79508 ( 24) covalent geometry : bond 0.00232 (18909) covalent geometry : angle 0.52023 (25565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 367 time to evaluate : 2.293 Fit side-chains revert: symmetry clash REVERT: H 115 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8537 (mp) REVERT: H 200 MET cc_start: 0.8016 (mmm) cc_final: 0.7807 (mmp) REVERT: F 99 ARG cc_start: 0.6609 (ptm160) cc_final: 0.5908 (ptm160) REVERT: F 126 GLU cc_start: 0.6513 (mt-10) cc_final: 0.5986 (tm-30) REVERT: C 502 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (tp) REVERT: C 641 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7364 (mttt) REVERT: C 714 GLN cc_start: 0.8430 (mm110) cc_final: 0.8228 (mm-40) REVERT: A 789 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9041 (tt) REVERT: D 816 TYR cc_start: 0.7419 (t80) cc_final: 0.7154 (t80) REVERT: E 5 ASP cc_start: 0.5686 (m-30) cc_final: 0.5235 (m-30) REVERT: E 6 ARG cc_start: 0.6066 (mmm-85) cc_final: 0.5513 (mmt180) REVERT: E 33 TRP cc_start: 0.8856 (m100) cc_final: 0.8624 (m100) REVERT: E 58 MET cc_start: 0.7228 (mtp) cc_final: 0.6758 (mtp) REVERT: E 78 LYS cc_start: 0.7287 (ptmt) cc_final: 0.6613 (pttt) REVERT: E 200 MET cc_start: 0.7268 (ptp) cc_final: 0.7027 (ptp) outliers start: 45 outliers final: 21 residues processed: 395 average time/residue: 0.3003 time to fit residues: 179.6162 Evaluate side-chains 359 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 121 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.7980 chunk 134 optimal weight: 0.0670 chunk 224 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.3120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 149 ASN B 756 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 207 GLN G 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.134119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095491 restraints weight = 111582.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100689 restraints weight = 35183.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102015 restraints weight = 17421.715| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18921 Z= 0.123 Angle : 0.521 8.903 25589 Z= 0.268 Chirality : 0.039 0.171 2877 Planarity : 0.004 0.068 3155 Dihedral : 3.541 54.816 2565 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.29 % Allowed : 24.23 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.18), residues: 2337 helix: 2.89 (0.14), residues: 1403 sheet: -0.57 (0.39), residues: 160 loop : -0.78 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP C 766 HIS 0.003 0.001 HIS F 60 PHE 0.013 0.001 PHE C 814 TYR 0.021 0.001 TYR B 673 ARG 0.007 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 1211) hydrogen bonds : angle 3.70269 ( 3526) SS BOND : bond 0.00312 ( 12) SS BOND : angle 1.20716 ( 24) covalent geometry : bond 0.00284 (18909) covalent geometry : angle 0.51978 (25565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 361 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 12 LEU cc_start: 0.7984 (mp) cc_final: 0.7666 (mp) REVERT: H 86 ASP cc_start: 0.0324 (OUTLIER) cc_final: -0.0251 (t70) REVERT: H 115 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8499 (mp) REVERT: H 199 HIS cc_start: 0.7832 (t70) cc_final: 0.7627 (t70) REVERT: F 99 ARG cc_start: 0.6573 (ptm160) cc_final: 0.6235 (ptm160) REVERT: F 120 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.6056 (pp) REVERT: F 126 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6213 (tm-30) REVERT: F 199 HIS cc_start: 0.8151 (t-90) cc_final: 0.7946 (t-90) REVERT: C 407 MET cc_start: 0.7046 (ptp) cc_final: 0.6710 (ptm) REVERT: C 641 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7379 (mttt) REVERT: B 496 MET cc_start: 0.8584 (ptm) cc_final: 0.8373 (ttp) REVERT: B 634 GLU cc_start: 0.7182 (tp30) cc_final: 0.6871 (tp30) REVERT: A 634 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7307 (tt0) REVERT: A 789 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9144 (tt) REVERT: D 816 TYR cc_start: 0.7391 (t80) cc_final: 0.7168 (t80) REVERT: E 5 ASP cc_start: 0.5636 (m-30) cc_final: 0.5275 (m-30) REVERT: E 33 TRP cc_start: 0.8903 (m100) cc_final: 0.8566 (m100) REVERT: E 58 MET cc_start: 0.7187 (mtp) cc_final: 0.6755 (mtp) REVERT: E 78 LYS cc_start: 0.7241 (ptmt) cc_final: 0.6627 (pttt) REVERT: G 70 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5503 (tp30) REVERT: G 72 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6632 (p0) outliers start: 64 outliers final: 36 residues processed: 403 average time/residue: 0.2889 time to fit residues: 175.0815 Evaluate side-chains 359 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 317 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 175 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090870 restraints weight = 83561.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095135 restraints weight = 30101.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097787 restraints weight = 17455.186| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 18921 Z= 0.200 Angle : 0.596 11.492 25589 Z= 0.307 Chirality : 0.042 0.189 2877 Planarity : 0.004 0.068 3155 Dihedral : 3.922 50.563 2565 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.95 % Allowed : 24.38 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.89 (0.18), residues: 2337 helix: 2.54 (0.14), residues: 1401 sheet: -0.75 (0.36), residues: 190 loop : -0.74 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 671 HIS 0.004 0.001 HIS F 60 PHE 0.017 0.002 PHE C 814 TYR 0.020 0.002 TYR C 424 ARG 0.007 0.001 ARG G 65 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 1211) hydrogen bonds : angle 3.94681 ( 3526) SS BOND : bond 0.00589 ( 12) SS BOND : angle 1.38120 ( 24) covalent geometry : bond 0.00472 (18909) covalent geometry : angle 0.59524 (25565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 345 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 ASP cc_start: 0.0254 (OUTLIER) cc_final: -0.0458 (t70) REVERT: H 199 HIS cc_start: 0.7849 (t70) cc_final: 0.7521 (t70) REVERT: C 407 MET cc_start: 0.7128 (ptp) cc_final: 0.6703 (ptm) REVERT: C 641 LYS cc_start: 0.8012 (ttpp) cc_final: 0.7449 (mttt) REVERT: C 710 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 814 PHE cc_start: 0.7962 (t80) cc_final: 0.7750 (t80) REVERT: B 634 GLU cc_start: 0.7208 (tp30) cc_final: 0.6844 (tp30) REVERT: B 702 TYR cc_start: 0.8237 (t80) cc_final: 0.7846 (t80) REVERT: A 634 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7342 (pt0) REVERT: A 705 GLU cc_start: 0.8095 (mp0) cc_final: 0.7892 (mp0) REVERT: A 789 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9211 (tt) REVERT: D 463 MET cc_start: 0.8322 (mmt) cc_final: 0.7051 (mmt) REVERT: D 816 TYR cc_start: 0.7569 (t80) cc_final: 0.7360 (t80) outliers start: 77 outliers final: 47 residues processed: 395 average time/residue: 0.3057 time to fit residues: 183.1649 Evaluate side-chains 366 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 678 GLU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 183 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 218 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 205 HIS C 756 GLN ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.134975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096843 restraints weight = 87850.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.102990 restraints weight = 32709.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103392 restraints weight = 16750.593| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18921 Z= 0.105 Angle : 0.516 10.475 25589 Z= 0.265 Chirality : 0.039 0.169 2877 Planarity : 0.004 0.056 3155 Dihedral : 3.493 21.607 2563 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.93 % Allowed : 25.21 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.18), residues: 2337 helix: 2.82 (0.14), residues: 1403 sheet: -0.43 (0.38), residues: 176 loop : -0.68 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 671 HIS 0.004 0.001 HIS D 412 PHE 0.014 0.001 PHE G 116 TYR 0.016 0.001 TYR B 673 ARG 0.006 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 1211) hydrogen bonds : angle 3.65676 ( 3526) SS BOND : bond 0.00415 ( 12) SS BOND : angle 1.50810 ( 24) covalent geometry : bond 0.00230 (18909) covalent geometry : angle 0.51409 (25565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 352 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6774 (p) cc_final: 0.6278 (p) REVERT: H 12 LEU cc_start: 0.8023 (mp) cc_final: 0.7679 (mp) REVERT: H 86 ASP cc_start: 0.0220 (OUTLIER) cc_final: -0.0526 (t70) REVERT: H 127 PHE cc_start: 0.5319 (OUTLIER) cc_final: 0.5006 (m-10) REVERT: H 199 HIS cc_start: 0.7813 (t70) cc_final: 0.7541 (t70) REVERT: H 204 ARG cc_start: 0.7043 (ttm-80) cc_final: 0.6336 (mtm110) REVERT: F 21 PHE cc_start: 0.7907 (t80) cc_final: 0.7561 (t80) REVERT: F 76 LEU cc_start: 0.6635 (mp) cc_final: 0.6134 (mm) REVERT: F 99 ARG cc_start: 0.6260 (ptm160) cc_final: 0.5568 (ptm160) REVERT: C 407 MET cc_start: 0.7147 (ptp) cc_final: 0.6852 (ptm) REVERT: C 441 LYS cc_start: 0.8463 (tmtt) cc_final: 0.7955 (mmmt) REVERT: C 641 LYS cc_start: 0.7844 (ttpp) cc_final: 0.7374 (mttt) REVERT: C 814 PHE cc_start: 0.7939 (t80) cc_final: 0.7650 (t80) REVERT: B 401 LEU cc_start: 0.8544 (mt) cc_final: 0.8100 (pt) REVERT: B 702 TYR cc_start: 0.8209 (t80) cc_final: 0.7844 (t80) REVERT: B 732 TYR cc_start: 0.8408 (m-10) cc_final: 0.8123 (m-10) REVERT: A 634 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7361 (pt0) REVERT: A 789 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9145 (tt) REVERT: D 463 MET cc_start: 0.8272 (mmt) cc_final: 0.7022 (mmt) REVERT: D 816 TYR cc_start: 0.7477 (t80) cc_final: 0.7253 (t80) REVERT: E 30 THR cc_start: 0.6938 (p) cc_final: 0.6679 (p) REVERT: E 58 MET cc_start: 0.7301 (mtp) cc_final: 0.6969 (mtp) REVERT: G 37 ARG cc_start: 0.5187 (ptt-90) cc_final: 0.4593 (ptt-90) outliers start: 57 outliers final: 34 residues processed: 391 average time/residue: 0.2952 time to fit residues: 176.5439 Evaluate side-chains 358 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 125 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 95 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 160 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095481 restraints weight = 94372.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101448 restraints weight = 34219.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102067 restraints weight = 17408.802| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18921 Z= 0.128 Angle : 0.530 11.389 25589 Z= 0.272 Chirality : 0.039 0.168 2877 Planarity : 0.004 0.061 3155 Dihedral : 3.526 30.941 2563 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.98 % Allowed : 25.05 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.24 (0.18), residues: 2337 helix: 2.85 (0.13), residues: 1399 sheet: -0.41 (0.38), residues: 176 loop : -0.72 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 671 HIS 0.007 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.014 0.001 TYR B 673 ARG 0.010 0.001 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 1211) hydrogen bonds : angle 3.68087 ( 3526) SS BOND : bond 0.00254 ( 12) SS BOND : angle 1.41379 ( 24) covalent geometry : bond 0.00298 (18909) covalent geometry : angle 0.52811 (25565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6781 (p) cc_final: 0.6253 (p) REVERT: H 12 LEU cc_start: 0.7977 (mp) cc_final: 0.7649 (mp) REVERT: H 86 ASP cc_start: 0.0214 (OUTLIER) cc_final: -0.0464 (t0) REVERT: H 127 PHE cc_start: 0.5473 (OUTLIER) cc_final: 0.5203 (m-10) REVERT: H 131 ARG cc_start: 0.5034 (mmp-170) cc_final: 0.4787 (mmm160) REVERT: H 204 ARG cc_start: 0.6758 (ttm-80) cc_final: 0.6367 (mtm110) REVERT: F 76 LEU cc_start: 0.6581 (mp) cc_final: 0.6261 (mm) REVERT: F 86 ASP cc_start: 0.1478 (OUTLIER) cc_final: 0.1159 (t70) REVERT: F 99 ARG cc_start: 0.6288 (ptm160) cc_final: 0.5634 (ptm160) REVERT: F 102 ARG cc_start: 0.6641 (tpt90) cc_final: 0.6340 (tpt170) REVERT: C 407 MET cc_start: 0.7148 (ptp) cc_final: 0.6733 (ptm) REVERT: C 641 LYS cc_start: 0.7904 (ttpp) cc_final: 0.7447 (mttt) REVERT: C 814 PHE cc_start: 0.7958 (t80) cc_final: 0.7712 (t80) REVERT: B 401 LEU cc_start: 0.8586 (mt) cc_final: 0.8092 (pt) REVERT: B 702 TYR cc_start: 0.8232 (t80) cc_final: 0.7922 (t80) REVERT: A 399 THR cc_start: 0.8880 (p) cc_final: 0.8535 (m) REVERT: A 634 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7402 (pt0) REVERT: A 705 GLU cc_start: 0.8060 (mp0) cc_final: 0.7804 (mp0) REVERT: A 789 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9170 (tt) REVERT: D 463 MET cc_start: 0.8268 (mmt) cc_final: 0.7043 (mmt) REVERT: D 816 TYR cc_start: 0.7490 (t80) cc_final: 0.7269 (t80) REVERT: E 30 THR cc_start: 0.7133 (p) cc_final: 0.6905 (p) REVERT: G 98 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7315 (mp) outliers start: 58 outliers final: 46 residues processed: 372 average time/residue: 0.2999 time to fit residues: 169.5850 Evaluate side-chains 368 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 84 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.133514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094739 restraints weight = 99150.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099457 restraints weight = 33041.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102414 restraints weight = 18466.443| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18921 Z= 0.126 Angle : 0.530 11.587 25589 Z= 0.272 Chirality : 0.039 0.169 2877 Planarity : 0.004 0.055 3155 Dihedral : 3.561 34.304 2563 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.49 % Allowed : 24.90 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.22 (0.18), residues: 2337 helix: 2.83 (0.13), residues: 1399 sheet: -0.52 (0.37), residues: 186 loop : -0.70 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.013 0.001 TYR B 673 ARG 0.007 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 1211) hydrogen bonds : angle 3.67843 ( 3526) SS BOND : bond 0.00302 ( 12) SS BOND : angle 1.54687 ( 24) covalent geometry : bond 0.00292 (18909) covalent geometry : angle 0.52822 (25565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 343 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6699 (p) cc_final: 0.6153 (p) REVERT: H 12 LEU cc_start: 0.8069 (mp) cc_final: 0.7727 (mp) REVERT: H 86 ASP cc_start: 0.0013 (OUTLIER) cc_final: -0.0618 (t0) REVERT: H 127 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.5145 (m-10) REVERT: H 204 ARG cc_start: 0.6784 (ttm-80) cc_final: 0.6525 (mtm110) REVERT: F 76 LEU cc_start: 0.6304 (mp) cc_final: 0.5889 (mm) REVERT: F 86 ASP cc_start: 0.1597 (OUTLIER) cc_final: 0.1220 (t70) REVERT: F 99 ARG cc_start: 0.6307 (ptm160) cc_final: 0.5778 (ptm160) REVERT: F 102 ARG cc_start: 0.6656 (tpt90) cc_final: 0.6235 (tpt170) REVERT: F 204 ARG cc_start: 0.6877 (ptm160) cc_final: 0.6567 (ptm160) REVERT: C 407 MET cc_start: 0.6938 (ptp) cc_final: 0.6690 (ptm) REVERT: C 641 LYS cc_start: 0.8029 (ttpp) cc_final: 0.7526 (mttt) REVERT: C 710 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 401 LEU cc_start: 0.8508 (mt) cc_final: 0.8053 (pt) REVERT: B 702 TYR cc_start: 0.8247 (t80) cc_final: 0.7982 (t80) REVERT: B 732 TYR cc_start: 0.8420 (m-10) cc_final: 0.8173 (m-10) REVERT: B 755 GLU cc_start: 0.8501 (mp0) cc_final: 0.7982 (mp0) REVERT: A 399 THR cc_start: 0.8823 (p) cc_final: 0.8485 (m) REVERT: A 634 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7404 (pt0) REVERT: A 705 GLU cc_start: 0.8028 (mp0) cc_final: 0.7781 (mp0) REVERT: A 789 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9166 (tt) REVERT: D 463 MET cc_start: 0.8205 (mmt) cc_final: 0.7060 (mmt) REVERT: D 633 ILE cc_start: 0.8744 (mm) cc_final: 0.8487 (tp) REVERT: D 816 TYR cc_start: 0.7536 (t80) cc_final: 0.7313 (t80) REVERT: E 30 THR cc_start: 0.6668 (p) cc_final: 0.6347 (p) REVERT: G 98 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7403 (mp) outliers start: 68 outliers final: 56 residues processed: 391 average time/residue: 0.2952 time to fit residues: 174.4020 Evaluate side-chains 388 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094308 restraints weight = 68900.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098443 restraints weight = 27265.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100962 restraints weight = 16608.015| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18921 Z= 0.111 Angle : 0.525 10.991 25589 Z= 0.269 Chirality : 0.039 0.165 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.478 31.878 2563 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.93 % Allowed : 25.36 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.29 (0.18), residues: 2337 helix: 2.88 (0.13), residues: 1401 sheet: -0.42 (0.38), residues: 176 loop : -0.67 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP B 671 HIS 0.006 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.013 0.001 TYR E 32 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 1211) hydrogen bonds : angle 3.61337 ( 3526) SS BOND : bond 0.00466 ( 12) SS BOND : angle 1.78956 ( 24) covalent geometry : bond 0.00252 (18909) covalent geometry : angle 0.52196 (25565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 342 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6658 (p) cc_final: 0.6163 (p) REVERT: H 12 LEU cc_start: 0.7981 (mp) cc_final: 0.7648 (mp) REVERT: H 58 MET cc_start: 0.6041 (tpt) cc_final: 0.5591 (mmm) REVERT: H 86 ASP cc_start: -0.0075 (OUTLIER) cc_final: -0.0571 (t0) REVERT: H 204 ARG cc_start: 0.6937 (ttm-80) cc_final: 0.6450 (mtm110) REVERT: F 76 LEU cc_start: 0.6271 (mp) cc_final: 0.5899 (mm) REVERT: F 86 ASP cc_start: 0.1635 (OUTLIER) cc_final: 0.1255 (t70) REVERT: F 99 ARG cc_start: 0.6357 (ptm160) cc_final: 0.5837 (ptm160) REVERT: F 102 ARG cc_start: 0.6596 (tpt90) cc_final: 0.6181 (tpt170) REVERT: C 407 MET cc_start: 0.6935 (ptp) cc_final: 0.6628 (ptm) REVERT: C 641 LYS cc_start: 0.7971 (ttpp) cc_final: 0.7517 (mttt) REVERT: C 642 GLN cc_start: 0.6408 (pp30) cc_final: 0.5718 (tm-30) REVERT: B 401 LEU cc_start: 0.8569 (mt) cc_final: 0.8069 (pt) REVERT: B 639 LEU cc_start: 0.8772 (tp) cc_final: 0.8553 (tt) REVERT: B 702 TYR cc_start: 0.8257 (t80) cc_final: 0.7962 (t80) REVERT: B 732 TYR cc_start: 0.8482 (m-10) cc_final: 0.8161 (m-10) REVERT: B 755 GLU cc_start: 0.8417 (mp0) cc_final: 0.8079 (mp0) REVERT: A 399 THR cc_start: 0.8781 (p) cc_final: 0.8457 (m) REVERT: A 634 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7373 (pt0) REVERT: A 789 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9134 (tt) REVERT: D 463 MET cc_start: 0.8227 (mmt) cc_final: 0.7042 (mmt) REVERT: D 633 ILE cc_start: 0.8774 (mm) cc_final: 0.8518 (tp) REVERT: D 816 TYR cc_start: 0.7494 (t80) cc_final: 0.7280 (t80) REVERT: E 30 THR cc_start: 0.6907 (p) cc_final: 0.6654 (p) REVERT: E 58 MET cc_start: 0.7439 (mtp) cc_final: 0.7198 (mtp) REVERT: G 98 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7376 (mp) REVERT: G 99 ARG cc_start: 0.5162 (ttm110) cc_final: 0.4343 (ptm160) outliers start: 57 outliers final: 49 residues processed: 382 average time/residue: 0.3021 time to fit residues: 175.3041 Evaluate side-chains 381 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 328 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 642 GLN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain G residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 212 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091005 restraints weight = 91046.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095301 restraints weight = 31596.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098084 restraints weight = 18090.716| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18921 Z= 0.151 Angle : 0.571 12.036 25589 Z= 0.291 Chirality : 0.040 0.175 2877 Planarity : 0.004 0.055 3155 Dihedral : 3.601 33.554 2563 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.44 % Allowed : 25.31 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.11 (0.18), residues: 2337 helix: 2.73 (0.14), residues: 1401 sheet: -0.62 (0.35), residues: 206 loop : -0.71 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.022 0.001 TYR C 816 ARG 0.007 0.001 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 1211) hydrogen bonds : angle 3.73388 ( 3526) SS BOND : bond 0.00341 ( 12) SS BOND : angle 1.85696 ( 24) covalent geometry : bond 0.00356 (18909) covalent geometry : angle 0.56811 (25565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 335 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6729 (p) cc_final: 0.6250 (p) REVERT: H 12 LEU cc_start: 0.7958 (mp) cc_final: 0.7631 (mp) REVERT: H 58 MET cc_start: 0.6144 (tpt) cc_final: 0.5663 (mmm) REVERT: H 86 ASP cc_start: 0.0139 (OUTLIER) cc_final: -0.0423 (t0) REVERT: H 204 ARG cc_start: 0.6924 (ttm-80) cc_final: 0.6364 (mtm110) REVERT: F 99 ARG cc_start: 0.6276 (ptm160) cc_final: 0.5711 (ptm160) REVERT: F 102 ARG cc_start: 0.6781 (tpt90) cc_final: 0.6276 (tpt170) REVERT: F 144 SER cc_start: 0.8505 (m) cc_final: 0.8244 (p) REVERT: C 407 MET cc_start: 0.6990 (ptp) cc_final: 0.6661 (ptm) REVERT: C 641 LYS cc_start: 0.8049 (ttpp) cc_final: 0.7613 (mttt) REVERT: C 642 GLN cc_start: 0.6487 (pp30) cc_final: 0.5811 (tm-30) REVERT: B 401 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8095 (pt) REVERT: B 702 TYR cc_start: 0.8304 (t80) cc_final: 0.8021 (t80) REVERT: B 755 GLU cc_start: 0.8391 (mp0) cc_final: 0.8075 (mp0) REVERT: A 399 THR cc_start: 0.8744 (p) cc_final: 0.8392 (m) REVERT: A 634 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7366 (pt0) REVERT: A 756 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: D 463 MET cc_start: 0.8214 (mmt) cc_final: 0.6957 (mmt) REVERT: D 633 ILE cc_start: 0.8784 (mm) cc_final: 0.8526 (tp) REVERT: D 816 TYR cc_start: 0.7519 (t80) cc_final: 0.7296 (t80) REVERT: E 30 THR cc_start: 0.7100 (p) cc_final: 0.6854 (p) REVERT: G 24 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7658 (mmt) REVERT: G 98 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7420 (mp) outliers start: 67 outliers final: 56 residues processed: 378 average time/residue: 0.2964 time to fit residues: 170.2602 Evaluate side-chains 385 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 756 GLN Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 68 CYS Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 109 optimal weight: 0.0470 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.130854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090985 restraints weight = 105266.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095588 restraints weight = 33923.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098491 restraints weight = 18708.053| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18921 Z= 0.133 Angle : 0.562 12.024 25589 Z= 0.286 Chirality : 0.039 0.168 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.590 33.536 2563 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.03 % Allowed : 25.82 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.12 (0.18), residues: 2337 helix: 2.75 (0.13), residues: 1401 sheet: -0.50 (0.37), residues: 186 loop : -0.75 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 671 HIS 0.005 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.018 0.001 TYR A 647 ARG 0.008 0.001 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 1211) hydrogen bonds : angle 3.70327 ( 3526) SS BOND : bond 0.00291 ( 12) SS BOND : angle 1.71562 ( 24) covalent geometry : bond 0.00313 (18909) covalent geometry : angle 0.56015 (25565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4674 Ramachandran restraints generated. 2337 Oldfield, 0 Emsley, 2337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 327 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 VAL cc_start: 0.6646 (p) cc_final: 0.6140 (p) REVERT: H 12 LEU cc_start: 0.7958 (mp) cc_final: 0.7630 (mp) REVERT: H 58 MET cc_start: 0.6147 (tpt) cc_final: 0.5665 (mmm) REVERT: H 86 ASP cc_start: 0.0272 (OUTLIER) cc_final: -0.0310 (t0) REVERT: H 204 ARG cc_start: 0.7095 (ttm-80) cc_final: 0.6497 (mtm110) REVERT: F 99 ARG cc_start: 0.6307 (ptm160) cc_final: 0.5765 (ptm160) REVERT: F 102 ARG cc_start: 0.6737 (tpt90) cc_final: 0.6254 (tpt170) REVERT: F 144 SER cc_start: 0.8529 (m) cc_final: 0.8287 (p) REVERT: C 407 MET cc_start: 0.6931 (ptp) cc_final: 0.6582 (ptm) REVERT: C 641 LYS cc_start: 0.7968 (ttpp) cc_final: 0.7537 (mttt) REVERT: C 642 GLN cc_start: 0.6446 (pp30) cc_final: 0.5777 (tm-30) REVERT: B 401 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8111 (pt) REVERT: B 634 GLU cc_start: 0.7394 (tp30) cc_final: 0.7168 (tp30) REVERT: B 702 TYR cc_start: 0.8281 (t80) cc_final: 0.8004 (t80) REVERT: B 732 TYR cc_start: 0.8497 (m-10) cc_final: 0.8219 (m-10) REVERT: B 755 GLU cc_start: 0.8362 (mp0) cc_final: 0.8037 (mp0) REVERT: A 399 THR cc_start: 0.8746 (p) cc_final: 0.8410 (m) REVERT: A 634 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7400 (pt0) REVERT: D 463 MET cc_start: 0.8217 (mmt) cc_final: 0.6926 (mmt) REVERT: D 633 ILE cc_start: 0.8770 (mm) cc_final: 0.8523 (tp) REVERT: D 816 TYR cc_start: 0.7501 (t80) cc_final: 0.7283 (t80) REVERT: E 30 THR cc_start: 0.7018 (p) cc_final: 0.6757 (p) REVERT: G 24 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7733 (mmt) REVERT: G 98 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7397 (mp) REVERT: G 99 ARG cc_start: 0.5208 (ttm110) cc_final: 0.4382 (ptm160) outliers start: 59 outliers final: 52 residues processed: 365 average time/residue: 0.2961 time to fit residues: 164.3471 Evaluate side-chains 374 residues out of total 1977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 591 ILE Chi-restraints excluded: chain C residue 669 LYS Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 773 CYS Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 546 PHE Chi-restraints excluded: chain D residue 729 SER Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 125 SER Chi-restraints excluded: chain G residue 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 202 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092901 restraints weight = 77076.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097098 restraints weight = 28855.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099750 restraints weight = 17158.574| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18921 Z= 0.117 Angle : 0.558 11.950 25589 Z= 0.282 Chirality : 0.039 0.165 2877 Planarity : 0.004 0.054 3155 Dihedral : 3.566 33.381 2563 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.82 % Allowed : 26.33 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2.15 (0.18), residues: 2337 helix: 2.77 (0.13), residues: 1401 sheet: -0.51 (0.37), residues: 186 loop : -0.72 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 671 HIS 0.006 0.001 HIS H 205 PHE 0.023 0.001 PHE D 546 TYR 0.022 0.001 TYR C 816 ARG 0.008 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 1211) hydrogen bonds : angle 3.68856 ( 3526) SS BOND : bond 0.00261 ( 12) SS BOND : angle 1.42893 ( 24) covalent geometry : bond 0.00268 (18909) covalent geometry : angle 0.55625 (25565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7386.76 seconds wall clock time: 129 minutes 28.62 seconds (7768.62 seconds total)