Starting phenix.real_space_refine on Tue Jun 24 15:24:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w8j_32357/06_2025/7w8j_32357.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w8j_32357/06_2025/7w8j_32357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w8j_32357/06_2025/7w8j_32357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w8j_32357/06_2025/7w8j_32357.map" model { file = "/net/cci-nas-00/data/ceres_data/7w8j_32357/06_2025/7w8j_32357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w8j_32357/06_2025/7w8j_32357.cif" } resolution = 2.5 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 100 5.16 5 C 17914 2.51 5 N 4990 2.21 5 O 5670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28678 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6006 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6122 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "C" Number of atoms: 6014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6113 Chain: "D" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "E" Number of atoms: 6014 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6113 Chain: "F" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "G" Number of atoms: 6006 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 Conformer: "B" Number of residues, atoms: 762, 5981 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 722} 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 bond proxies already assigned to first conformer: 6122 Chain: "H" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1086 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 27.90, per 1000 atoms: 0.97 Number of scatterers: 28678 At special positions: 0 Unit cell: (123.05, 153.01, 107, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 100 16.00 O 5670 8.00 N 4990 7.00 C 17914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 7.5 seconds 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6460 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 44 sheets defined 25.8% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.566A pdb=" N ARG A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.118A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 537 Processing helix chain 'A' and resid 594 through 597 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 623 through 631 removed outlier: 6.153A pdb=" N GLU A 628 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG A 629 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 716 through 718 No H-bonds generated for 'chain 'A' and resid 716 through 718' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.589A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 754 Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.544A pdb=" N ARG B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.355A pdb=" N GLU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.946A pdb=" N MET B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 131 Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.561A pdb=" N ARG C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 458 through 462 Processing helix chain 'C' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.119A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 537 Processing helix chain 'C' and resid 594 through 597 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 623 through 631 removed outlier: 6.164A pdb=" N GLU C 628 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG C 629 " --> pdb=" O GLN C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 Processing helix chain 'C' and resid 688 through 691 Processing helix chain 'C' and resid 716 through 718 No H-bonds generated for 'chain 'C' and resid 716 through 718' Processing helix chain 'C' and resid 726 through 733 removed outlier: 3.590A pdb=" N TRP C 729 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 730 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 733 " --> pdb=" O LEU C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 19 through 41 removed outlier: 3.541A pdb=" N ARG D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 removed outlier: 4.354A pdb=" N GLU D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 72 removed outlier: 3.944A pdb=" N MET D 72 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 131 Processing helix chain 'E' and resid 250 through 259 removed outlier: 3.561A pdb=" N ARG E 259 " --> pdb=" O GLU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 410 through 416 Processing helix chain 'E' and resid 422 through 431 Processing helix chain 'E' and resid 458 through 462 Processing helix chain 'E' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS E 480 " --> pdb=" O PRO E 476 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.118A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 Processing helix chain 'E' and resid 594 through 597 Processing helix chain 'E' and resid 600 through 605 Processing helix chain 'E' and resid 623 through 631 removed outlier: 6.164A pdb=" N GLU E 628 " --> pdb=" O SER E 625 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG E 629 " --> pdb=" O GLN E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 666 Processing helix chain 'E' and resid 688 through 691 Processing helix chain 'E' and resid 716 through 718 No H-bonds generated for 'chain 'E' and resid 716 through 718' Processing helix chain 'E' and resid 726 through 733 removed outlier: 3.591A pdb=" N TRP E 729 " --> pdb=" O SER E 726 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU E 730 " --> pdb=" O ILE E 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 733 " --> pdb=" O LEU E 730 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 739 Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 11 through 15 Processing helix chain 'F' and resid 19 through 41 removed outlier: 3.541A pdb=" N ARG F 29 " --> pdb=" O PHE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 removed outlier: 4.354A pdb=" N GLU F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 72 removed outlier: 3.943A pdb=" N MET F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 131 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.565A pdb=" N ARG G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 323 through 327 Processing helix chain 'G' and resid 392 through 399 Processing helix chain 'G' and resid 403 through 408 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 422 through 431 Processing helix chain 'G' and resid 458 through 462 Processing helix chain 'G' and resid 474 through 488 removed outlier: 3.576A pdb=" N HIS G 480 " --> pdb=" O PRO G 476 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 4.119A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 537 Processing helix chain 'G' and resid 594 through 597 Processing helix chain 'G' and resid 600 through 605 Processing helix chain 'G' and resid 623 through 631 removed outlier: 6.153A pdb=" N GLU G 628 " --> pdb=" O SER G 625 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG G 629 " --> pdb=" O GLN G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 666 Processing helix chain 'G' and resid 688 through 691 Processing helix chain 'G' and resid 716 through 718 No H-bonds generated for 'chain 'G' and resid 716 through 718' Processing helix chain 'G' and resid 726 through 733 removed outlier: 3.589A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU G 733 " --> pdb=" O LEU G 730 " (cutoff:3.500A) Processing helix chain 'G' and resid 734 through 739 Processing helix chain 'G' and resid 740 through 754 Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'H' and resid 19 through 41 removed outlier: 3.544A pdb=" N ARG H 29 " --> pdb=" O PHE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.355A pdb=" N GLU H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 72 removed outlier: 3.945A pdb=" N MET H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 131 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 3.586A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL A 39 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 58 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU A 41 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 56 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE A 128 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY A 111 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE A 128 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY A 111 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA A 329 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY A 307 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.506A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N PHE A 611 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ARG A 660 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 11.711A pdb=" N PHE A 613 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N LEU A 658 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N HIS A 615 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR A 656 " --> pdb=" O HIS A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.506A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 611 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 420 through 421 removed outlier: 6.513A pdb=" N ALA B 89 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 523 removed outlier: 4.405A pdb=" N GLY A 591 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 6 through 10 removed outlier: 3.586A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL C 39 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 58 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU C 41 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLU C 56 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL C 239 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP C 101 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE C 128 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY C 111 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA C 329 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 307 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB9, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.450A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.578A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.526A pdb=" N ALA D 89 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC4, first strand: chain 'C' and resid 522 through 523 removed outlier: 4.408A pdb=" N GLY C 591 " --> pdb=" O ILE C 552 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 6 through 10 removed outlier: 3.585A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N VAL E 39 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 58 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU E 41 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU E 56 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 14 through 15 removed outlier: 5.204A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.331A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.331A pdb=" N ILE E 128 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY E 111 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA E 329 " --> pdb=" O GLY E 307 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY E 307 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 219 through 220 Processing sheet with id=AD2, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.451A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.578A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.715A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.505A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 420 through 421 removed outlier: 6.526A pdb=" N ALA F 89 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 451 through 453 Processing sheet with id=AD6, first strand: chain 'E' and resid 522 through 523 removed outlier: 4.407A pdb=" N GLY E 591 " --> pdb=" O ILE E 552 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 6 through 10 removed outlier: 3.586A pdb=" N PHE G 346 " --> pdb=" O PHE G 23 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL G 39 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE G 58 " --> pdb=" O VAL G 39 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU G 41 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU G 56 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.202A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE G 128 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY G 111 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 144 through 148 removed outlier: 6.330A pdb=" N ILE G 128 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLY G 111 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.122A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ALA G 329 " --> pdb=" O GLY G 307 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY G 307 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AE4, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.507A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N PHE G 611 " --> pdb=" O ARG G 660 " (cutoff:3.500A) removed outlier: 12.584A pdb=" N ARG G 660 " --> pdb=" O PHE G 611 " (cutoff:3.500A) removed outlier: 11.712A pdb=" N PHE G 613 " --> pdb=" O LEU G 658 " (cutoff:3.500A) removed outlier: 12.214A pdb=" N LEU G 658 " --> pdb=" O PHE G 613 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N HIS G 615 " --> pdb=" O TYR G 656 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR G 656 " --> pdb=" O HIS G 615 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.507A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE G 611 " --> pdb=" O THR G 685 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 420 through 421 removed outlier: 6.513A pdb=" N ALA H 89 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AE8, first strand: chain 'G' and resid 522 through 523 removed outlier: 4.404A pdb=" N GLY G 591 " --> pdb=" O ILE G 552 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3352 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: 18.33 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5546 1.33 - 1.45: 7854 1.45 - 1.58: 15646 1.58 - 1.71: 0 1.71 - 1.84: 164 Bond restraints: 29210 Sorted by residual: bond pdb=" N ARG C 264 " pdb=" CA ARG C 264 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 2.00e+01 bond pdb=" N ARG E 264 " pdb=" CA ARG E 264 " ideal model delta sigma weight residual 1.460 1.492 -0.032 7.10e-03 1.98e+04 2.00e+01 bond pdb=" N ILE G 603 " pdb=" CA ILE G 603 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 1.95e+01 bond pdb=" N ILE A 603 " pdb=" CA ILE A 603 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 1.95e+01 bond pdb=" N ARG G 264 " pdb=" CA ARG G 264 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.10e-03 1.98e+04 1.85e+01 ... (remaining 29205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 24628 1.41 - 2.82: 11724 2.82 - 4.23: 2951 4.23 - 5.64: 387 5.64 - 7.05: 24 Bond angle restraints: 39714 Sorted by residual: angle pdb=" CA ASP A 537 " pdb=" CB ASP A 537 " pdb=" CG ASP A 537 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.00e+00 1.00e+00 4.70e+01 angle pdb=" CA ASP G 537 " pdb=" CB ASP G 537 " pdb=" CG ASP G 537 " ideal model delta sigma weight residual 112.60 119.42 -6.82 1.00e+00 1.00e+00 4.66e+01 angle pdb=" C ARG C 447 " pdb=" N GLY C 448 " pdb=" CA GLY C 448 " ideal model delta sigma weight residual 120.10 124.92 -4.82 9.50e-01 1.11e+00 2.57e+01 angle pdb=" C ARG E 447 " pdb=" N GLY E 448 " pdb=" CA GLY E 448 " ideal model delta sigma weight residual 120.10 124.92 -4.82 9.50e-01 1.11e+00 2.57e+01 angle pdb=" C ARG C 660 " pdb=" N TYR C 661 " pdb=" CA TYR C 661 " ideal model delta sigma weight residual 120.95 128.00 -7.05 1.40e+00 5.10e-01 2.53e+01 ... (remaining 39709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15710 17.91 - 35.82: 1014 35.82 - 53.72: 192 53.72 - 71.63: 86 71.63 - 89.54: 52 Dihedral angle restraints: 17054 sinusoidal: 6838 harmonic: 10216 Sorted by residual: dihedral pdb=" CA SER C 114 " pdb=" C SER C 114 " pdb=" N ARG C 115 " pdb=" CA ARG C 115 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA SER E 114 " pdb=" C SER E 114 " pdb=" N ARG E 115 " pdb=" CA ARG E 115 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA SER A 114 " pdb=" C SER A 114 " pdb=" N ARG A 115 " pdb=" CA ARG A 115 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 17051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1361 0.042 - 0.084: 1260 0.084 - 0.126: 890 0.126 - 0.168: 411 0.168 - 0.210: 100 Chirality restraints: 4022 Sorted by residual: chirality pdb=" CA ARG E 31 " pdb=" N ARG E 31 " pdb=" C ARG E 31 " pdb=" CB ARG E 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG C 31 " pdb=" N ARG C 31 " pdb=" C ARG C 31 " pdb=" CB ARG C 31 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 4019 not shown) Planarity restraints: 5284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 740 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" CG ASN G 740 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN G 740 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN G 740 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 740 " 0.023 2.00e-02 2.50e+03 4.58e-02 2.10e+01 pdb=" CG ASN A 740 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 740 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 740 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 370 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" CG ASP C 370 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASP C 370 " 0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP C 370 " 0.021 2.00e-02 2.50e+03 ... (remaining 5281 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 18552 3.11 - 3.70: 45639 3.70 - 4.30: 71356 4.30 - 4.90: 115454 Nonbonded interactions: 251132 Sorted by model distance: nonbonded pdb=" OH TYR A 440 " pdb="FE FE A 801 " model vdw 1.909 2.260 nonbonded pdb=" OH TYR G 440 " pdb="FE FE G 801 " model vdw 1.909 2.260 nonbonded pdb=" OH TYR C 440 " pdb="FE FE C 801 " model vdw 1.911 2.260 nonbonded pdb=" OH TYR E 440 " pdb="FE FE E 801 " model vdw 1.912 2.260 nonbonded pdb=" OH TYR A 399 " pdb="FE FE A 801 " model vdw 1.914 2.260 ... (remaining 251127 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) selection = (chain 'C' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) selection = (chain 'E' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) selection = (chain 'G' and (resid 1 through 14 or resid 16 through 131 or resid 133 through \ 509 or resid 511 through 548 or resid 550 through 587 or resid 589 through 762 o \ r resid 801)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 91.150 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 : 0.014 0.057 29210 Z= 1.041 Angle : 1.616 7.046 39714 Z= 1.200 Chirality : 0.082 0.210 4022 Planarity : 0.004 0.046 5284 Dihedral : 14.207 89.538 10594 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.24 % Allowed : 4.51 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 3550 helix: -0.07 (0.18), residues: 660 sheet: 0.14 (0.20), residues: 684 loop : -0.34 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 22 HIS 0.019 0.002 HIS A 322 PHE 0.033 0.002 PHE F 53 TYR 0.037 0.003 TYR D 90 ARG 0.030 0.001 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.18366 ( 1020) hydrogen bonds : angle 7.32139 ( 3352) covalent geometry : bond 0.01362 (29210) covalent geometry : angle 1.61564 (39714) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 402 time to evaluate : 3.030 Fit side-chains REVERT: A 22 ARG cc_start: 0.8131 (mtm-85) cc_final: 0.7810 (mtm180) REVERT: A 211 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 255 GLU cc_start: 0.7409 (tp30) cc_final: 0.6880 (mm-30) REVERT: A 345 ASP cc_start: 0.7973 (m-30) cc_final: 0.7548 (m-30) REVERT: A 347 GLU cc_start: 0.7814 (pt0) cc_final: 0.7562 (pt0) REVERT: A 364 ARG cc_start: 0.6861 (mtm-85) cc_final: 0.6407 (mtm-85) REVERT: A 409 ASP cc_start: 0.6899 (m-30) cc_final: 0.6682 (m-30) REVERT: A 537 ASP cc_start: 0.7016 (p0) cc_final: 0.6743 (m-30) REVERT: A 588 ARG cc_start: 0.7433 (mmt90) cc_final: 0.6654 (mtp180) REVERT: A 627 ASP cc_start: 0.7343 (t0) cc_final: 0.6628 (t0) REVERT: A 641 GLU cc_start: 0.6341 (mt-10) cc_final: 0.6037 (mt-10) REVERT: A 659 ASP cc_start: 0.7944 (m-30) cc_final: 0.7676 (m-30) REVERT: A 717 ASN cc_start: 0.7407 (t0) cc_final: 0.6768 (t0) REVERT: A 736 ASN cc_start: 0.7962 (t0) cc_final: 0.7672 (t0) REVERT: A 745 MET cc_start: 0.8314 (ttm) cc_final: 0.7944 (ttm) REVERT: A 756 ASP cc_start: 0.7319 (m-30) cc_final: 0.6550 (p0) REVERT: A 757 GLU cc_start: 0.7295 (tt0) cc_final: 0.6984 (tt0) REVERT: B 11 ASP cc_start: 0.7169 (t0) cc_final: 0.6545 (t70) REVERT: B 28 GLU cc_start: 0.6688 (tp30) cc_final: 0.6442 (tp30) REVERT: B 62 TYR cc_start: 0.7517 (m-80) cc_final: 0.7132 (m-80) REVERT: B 90 TYR cc_start: 0.8302 (m-80) cc_final: 0.7591 (m-80) REVERT: B 110 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7762 (mptm) REVERT: C 31 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7528 (ttp-170) REVERT: C 63 GLU cc_start: 0.7606 (tt0) cc_final: 0.7350 (tt0) REVERT: C 130 ASP cc_start: 0.6212 (t70) cc_final: 0.5895 (t70) REVERT: C 225 GLN cc_start: 0.6846 (mt0) cc_final: 0.5832 (pp30) REVERT: C 264 ARG cc_start: 0.7522 (mtt180) cc_final: 0.7155 (mtp180) REVERT: C 299 ARG cc_start: 0.6978 (mtp85) cc_final: 0.6042 (tpt170) REVERT: C 343 GLU cc_start: 0.7160 (tt0) cc_final: 0.6779 (mm-30) REVERT: C 506 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6545 (mp0) REVERT: C 628 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6652 (tp30) REVERT: C 737 ASP cc_start: 0.7141 (t0) cc_final: 0.6695 (t70) REVERT: C 757 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6835 (mt-10) REVERT: D 11 ASP cc_start: 0.7786 (t0) cc_final: 0.7136 (t0) REVERT: D 14 ASN cc_start: 0.7776 (m-40) cc_final: 0.7475 (m-40) REVERT: D 28 GLU cc_start: 0.6655 (tt0) cc_final: 0.6438 (tp30) REVERT: D 36 ASP cc_start: 0.6830 (m-30) cc_final: 0.6490 (m-30) REVERT: D 78 ARG cc_start: 0.8392 (ptm160) cc_final: 0.8161 (ttm-80) REVERT: E 31 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7443 (ttp-170) REVERT: E 63 GLU cc_start: 0.7608 (tt0) cc_final: 0.7354 (tt0) REVERT: E 130 ASP cc_start: 0.6205 (t70) cc_final: 0.5915 (t70) REVERT: E 211 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7385 (mt-10) REVERT: E 225 GLN cc_start: 0.6846 (mt0) cc_final: 0.5832 (pp30) REVERT: E 264 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7157 (mtp180) REVERT: E 299 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6039 (tpt170) REVERT: E 343 GLU cc_start: 0.7168 (tt0) cc_final: 0.6783 (mm-30) REVERT: E 506 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6547 (mp0) REVERT: E 628 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6651 (tp30) REVERT: E 737 ASP cc_start: 0.7143 (t0) cc_final: 0.6696 (t70) REVERT: E 757 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6864 (mt-10) REVERT: F 11 ASP cc_start: 0.7806 (t0) cc_final: 0.7131 (t0) REVERT: F 14 ASN cc_start: 0.7777 (m-40) cc_final: 0.7436 (m-40) REVERT: F 28 GLU cc_start: 0.6651 (tt0) cc_final: 0.6435 (tp30) REVERT: F 36 ASP cc_start: 0.6829 (m-30) cc_final: 0.6489 (m-30) REVERT: F 78 ARG cc_start: 0.8388 (ptm160) cc_final: 0.8162 (ttm-80) REVERT: G 22 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7809 (mtm180) REVERT: G 211 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7201 (mt-10) REVERT: G 255 GLU cc_start: 0.7426 (tp30) cc_final: 0.6892 (mm-30) REVERT: G 345 ASP cc_start: 0.7966 (m-30) cc_final: 0.7546 (m-30) REVERT: G 347 GLU cc_start: 0.7818 (pt0) cc_final: 0.7565 (pt0) REVERT: G 364 ARG cc_start: 0.6862 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: G 409 ASP cc_start: 0.6907 (m-30) cc_final: 0.6688 (m-30) REVERT: G 537 ASP cc_start: 0.7020 (p0) cc_final: 0.6742 (m-30) REVERT: G 588 ARG cc_start: 0.7448 (mmt90) cc_final: 0.6671 (mtp180) REVERT: G 627 ASP cc_start: 0.7345 (t0) cc_final: 0.6632 (t0) REVERT: G 641 GLU cc_start: 0.6334 (mt-10) cc_final: 0.6034 (mt-10) REVERT: G 659 ASP cc_start: 0.7944 (m-30) cc_final: 0.7677 (m-30) REVERT: G 717 ASN cc_start: 0.7407 (t0) cc_final: 0.6769 (t0) REVERT: G 736 ASN cc_start: 0.7963 (t0) cc_final: 0.7673 (t0) REVERT: G 745 MET cc_start: 0.8316 (ttm) cc_final: 0.7947 (ttm) REVERT: G 756 ASP cc_start: 0.7318 (m-30) cc_final: 0.6551 (p0) REVERT: G 757 GLU cc_start: 0.7296 (tt0) cc_final: 0.6986 (tt0) REVERT: H 11 ASP cc_start: 0.7172 (t0) cc_final: 0.6548 (t70) REVERT: H 28 GLU cc_start: 0.6692 (tp30) cc_final: 0.6440 (tp30) REVERT: H 62 TYR cc_start: 0.7517 (m-80) cc_final: 0.7134 (m-80) REVERT: H 90 TYR cc_start: 0.8301 (m-80) cc_final: 0.7591 (m-80) REVERT: H 110 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7762 (mptm) outliers start: 4 outliers final: 0 residues processed: 406 average time/residue: 1.9924 time to fit residues: 916.8258 Evaluate side-chains 302 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN C 412 GLN C 431 ASN C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 HIS E 65 GLN E 125 ASN E 412 GLN E 431 ASN E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.085677 restraints weight = 104130.437| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.58 r_work: 0.2756 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29210 Z= 0.113 Angle : 0.539 6.984 39714 Z= 0.294 Chirality : 0.044 0.179 4022 Planarity : 0.004 0.033 5284 Dihedral : 4.456 25.278 4010 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.22 % Allowed : 6.59 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3550 helix: 1.93 (0.20), residues: 676 sheet: 0.24 (0.19), residues: 776 loop : -0.00 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 22 HIS 0.004 0.001 HIS G 234 PHE 0.014 0.002 PHE H 120 TYR 0.026 0.001 TYR A 661 ARG 0.004 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 1020) hydrogen bonds : angle 5.17684 ( 3352) covalent geometry : bond 0.00233 (29210) covalent geometry : angle 0.53922 (39714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 3.041 Fit side-chains REVERT: A 211 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8267 (mt-10) REVERT: A 445 ASP cc_start: 0.8176 (m-30) cc_final: 0.7930 (m-30) REVERT: A 491 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7809 (mm-30) REVERT: A 497 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8162 (mt-10) REVERT: A 537 ASP cc_start: 0.7970 (p0) cc_final: 0.7680 (m-30) REVERT: A 641 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6777 (mt-10) REVERT: A 717 ASN cc_start: 0.8022 (t0) cc_final: 0.7211 (t0) REVERT: A 736 ASN cc_start: 0.8181 (t0) cc_final: 0.7925 (t0) REVERT: A 737 ASP cc_start: 0.7991 (t0) cc_final: 0.7324 (t0) REVERT: A 745 MET cc_start: 0.8901 (ttm) cc_final: 0.8628 (ttm) REVERT: A 757 GLU cc_start: 0.7807 (tt0) cc_final: 0.7605 (tt0) REVERT: B 11 ASP cc_start: 0.8097 (t0) cc_final: 0.7710 (t70) REVERT: B 62 TYR cc_start: 0.8416 (m-80) cc_final: 0.8132 (m-80) REVERT: B 90 TYR cc_start: 0.8857 (m-80) cc_final: 0.8355 (m-80) REVERT: B 110 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8109 (mptm) REVERT: C 168 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7341 (tp30) REVERT: C 264 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7914 (mtt180) REVERT: C 299 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7777 (tpt170) REVERT: C 628 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7426 (tp30) REVERT: C 737 ASP cc_start: 0.8135 (t0) cc_final: 0.7674 (t70) REVERT: D 27 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8038 (m-30) REVERT: D 28 GLU cc_start: 0.8051 (tt0) cc_final: 0.7818 (tt0) REVERT: D 32 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8352 (mttm) REVERT: D 78 ARG cc_start: 0.8777 (ptm160) cc_final: 0.8544 (ttm-80) REVERT: E 168 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7400 (tp30) REVERT: E 211 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8170 (mt-10) REVERT: E 264 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7898 (mtt180) REVERT: E 299 ARG cc_start: 0.8403 (mtp85) cc_final: 0.7782 (tpt170) REVERT: E 628 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7447 (tp30) REVERT: E 737 ASP cc_start: 0.8147 (t0) cc_final: 0.7685 (t70) REVERT: F 27 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: F 28 GLU cc_start: 0.8091 (tt0) cc_final: 0.7866 (tt0) REVERT: F 32 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8348 (mttm) REVERT: F 78 ARG cc_start: 0.8791 (ptm160) cc_final: 0.8550 (ttm-80) REVERT: G 445 ASP cc_start: 0.8163 (m-30) cc_final: 0.7916 (m-30) REVERT: G 491 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: G 497 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8165 (mt-10) REVERT: G 537 ASP cc_start: 0.7985 (p0) cc_final: 0.7691 (m-30) REVERT: G 641 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6796 (mt-10) REVERT: G 717 ASN cc_start: 0.8041 (t0) cc_final: 0.7233 (t0) REVERT: G 736 ASN cc_start: 0.8172 (t0) cc_final: 0.7918 (t0) REVERT: G 737 ASP cc_start: 0.7990 (t0) cc_final: 0.7317 (t0) REVERT: G 745 MET cc_start: 0.8910 (ttm) cc_final: 0.8640 (ttm) REVERT: G 757 GLU cc_start: 0.7807 (tt0) cc_final: 0.7596 (tt0) REVERT: H 11 ASP cc_start: 0.8112 (t0) cc_final: 0.7716 (t70) REVERT: H 62 TYR cc_start: 0.8425 (m-80) cc_final: 0.8147 (m-80) REVERT: H 90 TYR cc_start: 0.8860 (m-80) cc_final: 0.8364 (m-80) REVERT: H 110 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8116 (mptm) outliers start: 32 outliers final: 11 residues processed: 346 average time/residue: 1.7880 time to fit residues: 705.9525 Evaluate side-chains 298 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 83 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 265 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 73 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 HIS E 65 GLN E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.098167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.080290 restraints weight = 110138.634| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.72 r_work: 0.2659 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29210 Z= 0.222 Angle : 0.652 8.244 39714 Z= 0.354 Chirality : 0.050 0.192 4022 Planarity : 0.005 0.048 5284 Dihedral : 4.977 25.094 4010 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.66 % Allowed : 8.04 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3550 helix: 1.71 (0.20), residues: 676 sheet: 0.28 (0.19), residues: 756 loop : -0.07 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 22 HIS 0.006 0.002 HIS A 97 PHE 0.018 0.003 PHE A 187 TYR 0.030 0.002 TYR A 661 ARG 0.005 0.001 ARG G 707 Details of bonding type rmsd hydrogen bonds : bond 0.05476 ( 1020) hydrogen bonds : angle 5.31952 ( 3352) covalent geometry : bond 0.00517 (29210) covalent geometry : angle 0.65179 (39714) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 300 time to evaluate : 3.035 Fit side-chains REVERT: A 445 ASP cc_start: 0.8392 (m-30) cc_final: 0.8091 (m-30) REVERT: A 491 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: A 506 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7805 (tp30) REVERT: A 717 ASN cc_start: 0.8234 (t0) cc_final: 0.7948 (t0) REVERT: A 736 ASN cc_start: 0.8271 (t0) cc_final: 0.8021 (t0) REVERT: B 11 ASP cc_start: 0.8137 (t0) cc_final: 0.7933 (t70) REVERT: B 62 TYR cc_start: 0.8544 (m-80) cc_final: 0.8205 (m-80) REVERT: B 90 TYR cc_start: 0.8916 (m-80) cc_final: 0.8318 (m-80) REVERT: B 110 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8184 (mmmt) REVERT: C 299 ARG cc_start: 0.8438 (mtp85) cc_final: 0.7828 (tpt170) REVERT: C 737 ASP cc_start: 0.8248 (t0) cc_final: 0.7865 (t70) REVERT: D 60 SER cc_start: 0.8637 (t) cc_final: 0.8351 (p) REVERT: D 78 ARG cc_start: 0.8908 (ptm160) cc_final: 0.8644 (ttm-80) REVERT: D 112 GLU cc_start: 0.7529 (pt0) cc_final: 0.7254 (pt0) REVERT: E 299 ARG cc_start: 0.8456 (mtp85) cc_final: 0.7828 (tpt170) REVERT: E 737 ASP cc_start: 0.8248 (t0) cc_final: 0.7860 (t70) REVERT: F 60 SER cc_start: 0.8645 (t) cc_final: 0.8361 (p) REVERT: F 78 ARG cc_start: 0.8908 (ptm160) cc_final: 0.8646 (ttm-80) REVERT: F 112 GLU cc_start: 0.7601 (pt0) cc_final: 0.7347 (pt0) REVERT: G 445 ASP cc_start: 0.8374 (m-30) cc_final: 0.8070 (m-30) REVERT: G 491 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: G 506 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: G 717 ASN cc_start: 0.8231 (t0) cc_final: 0.7943 (t0) REVERT: G 736 ASN cc_start: 0.8254 (t0) cc_final: 0.8004 (t0) REVERT: H 11 ASP cc_start: 0.8137 (t0) cc_final: 0.7932 (t70) REVERT: H 62 TYR cc_start: 0.8550 (m-80) cc_final: 0.8212 (m-80) REVERT: H 90 TYR cc_start: 0.8916 (m-80) cc_final: 0.8317 (m-80) REVERT: H 110 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8176 (mmmt) outliers start: 45 outliers final: 21 residues processed: 325 average time/residue: 2.2760 time to fit residues: 854.6978 Evaluate side-chains 313 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 288 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 506 GLU Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 65 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 257 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.081477 restraints weight = 107738.354| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.73 r_work: 0.2675 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2542 r_free = 0.2542 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29210 Z= 0.182 Angle : 0.601 8.151 39714 Z= 0.326 Chirality : 0.048 0.183 4022 Planarity : 0.005 0.040 5284 Dihedral : 4.866 24.577 4010 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.70 % Allowed : 8.96 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.14), residues: 3550 helix: 1.82 (0.20), residues: 656 sheet: 0.28 (0.20), residues: 756 loop : -0.09 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 473 HIS 0.006 0.001 HIS C 97 PHE 0.015 0.002 PHE A 187 TYR 0.031 0.002 TYR A 661 ARG 0.005 0.001 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 1020) hydrogen bonds : angle 5.14684 ( 3352) covalent geometry : bond 0.00418 (29210) covalent geometry : angle 0.60070 (39714) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 2.999 Fit side-chains revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8339 (m-30) cc_final: 0.7989 (m-30) REVERT: A 491 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: A 717 ASN cc_start: 0.8251 (t0) cc_final: 0.7532 (t0) REVERT: A 736 ASN cc_start: 0.8223 (t0) cc_final: 0.7984 (t0) REVERT: B 62 TYR cc_start: 0.8485 (m-80) cc_final: 0.8137 (m-80) REVERT: B 90 TYR cc_start: 0.8907 (m-80) cc_final: 0.8207 (m-80) REVERT: B 110 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8129 (mmmt) REVERT: B 116 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8139 (mtt) REVERT: C 62 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8162 (tt) REVERT: C 299 ARG cc_start: 0.8476 (mtp85) cc_final: 0.7819 (tpt170) REVERT: D 60 SER cc_start: 0.8639 (t) cc_final: 0.8350 (p) REVERT: D 78 ARG cc_start: 0.8942 (ptm160) cc_final: 0.8640 (ttm-80) REVERT: D 112 GLU cc_start: 0.7468 (pt0) cc_final: 0.7234 (pt0) REVERT: D 130 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7066 (tp30) REVERT: E 29 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: E 62 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (tt) REVERT: E 299 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7833 (tpt170) REVERT: F 60 SER cc_start: 0.8639 (t) cc_final: 0.8358 (p) REVERT: F 78 ARG cc_start: 0.8939 (ptm160) cc_final: 0.8710 (ttm-80) REVERT: F 112 GLU cc_start: 0.7601 (pt0) cc_final: 0.7377 (pt0) REVERT: F 130 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7074 (tp30) REVERT: G 445 ASP cc_start: 0.8340 (m-30) cc_final: 0.7990 (m-30) REVERT: G 491 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7997 (mm-30) REVERT: G 717 ASN cc_start: 0.8251 (t0) cc_final: 0.7529 (t0) REVERT: G 736 ASN cc_start: 0.8234 (t0) cc_final: 0.7998 (t0) REVERT: H 62 TYR cc_start: 0.8487 (m-80) cc_final: 0.8142 (m-80) REVERT: H 90 TYR cc_start: 0.8911 (m-80) cc_final: 0.8198 (m-80) REVERT: H 110 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8117 (mmmt) REVERT: H 116 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8158 (mtt) outliers start: 44 outliers final: 23 residues processed: 310 average time/residue: 1.7081 time to fit residues: 605.5461 Evaluate side-chains 320 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 3.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 60 optimal weight: 10.0000 chunk 334 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 260 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 278 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.079751 restraints weight = 106055.171| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.71 r_work: 0.2638 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29210 Z= 0.227 Angle : 0.647 7.962 39714 Z= 0.351 Chirality : 0.050 0.187 4022 Planarity : 0.005 0.050 5284 Dihedral : 5.039 24.394 4010 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.21 % Allowed : 8.96 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3550 helix: 1.73 (0.20), residues: 648 sheet: 0.29 (0.19), residues: 744 loop : -0.15 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 22 HIS 0.007 0.002 HIS E 97 PHE 0.018 0.003 PHE A 187 TYR 0.031 0.002 TYR A 661 ARG 0.005 0.001 ARG F 122 Details of bonding type rmsd hydrogen bonds : bond 0.05361 ( 1020) hydrogen bonds : angle 5.25925 ( 3352) covalent geometry : bond 0.00530 (29210) covalent geometry : angle 0.64745 (39714) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 3.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8389 (m-30) cc_final: 0.8017 (m-30) REVERT: A 447 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8191 (tmm-80) REVERT: A 491 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: A 717 ASN cc_start: 0.8303 (t0) cc_final: 0.8036 (t0) REVERT: A 736 ASN cc_start: 0.8253 (t0) cc_final: 0.8021 (t0) REVERT: B 62 TYR cc_start: 0.8548 (m-80) cc_final: 0.8162 (m-80) REVERT: B 90 TYR cc_start: 0.8941 (m-80) cc_final: 0.8262 (m-80) REVERT: B 110 LYS cc_start: 0.8438 (mmmt) cc_final: 0.7868 (mmtm) REVERT: B 116 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8130 (mtt) REVERT: C 29 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: C 62 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8265 (tt) REVERT: C 168 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7387 (tp30) REVERT: C 299 ARG cc_start: 0.8487 (mtp85) cc_final: 0.7835 (tpt170) REVERT: D 40 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: D 60 SER cc_start: 0.8764 (t) cc_final: 0.8444 (p) REVERT: D 78 ARG cc_start: 0.8974 (ptm160) cc_final: 0.8751 (ttm-80) REVERT: D 112 GLU cc_start: 0.7620 (pt0) cc_final: 0.7412 (pt0) REVERT: D 130 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7082 (tp30) REVERT: E 29 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: E 62 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8272 (tt) REVERT: E 168 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7422 (tp30) REVERT: E 299 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7836 (tpt170) REVERT: F 60 SER cc_start: 0.8755 (t) cc_final: 0.8444 (p) REVERT: F 78 ARG cc_start: 0.8968 (ptm160) cc_final: 0.8747 (ttm-80) REVERT: F 112 GLU cc_start: 0.7722 (pt0) cc_final: 0.7520 (pt0) REVERT: F 130 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7079 (tp30) REVERT: G 445 ASP cc_start: 0.8394 (m-30) cc_final: 0.8022 (m-30) REVERT: G 447 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8158 (tmm-80) REVERT: G 491 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: G 635 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: G 717 ASN cc_start: 0.8301 (t0) cc_final: 0.8033 (t0) REVERT: G 736 ASN cc_start: 0.8260 (t0) cc_final: 0.8029 (t0) REVERT: H 62 TYR cc_start: 0.8555 (m-80) cc_final: 0.8168 (m-80) REVERT: H 90 TYR cc_start: 0.8944 (m-80) cc_final: 0.8254 (m-80) REVERT: H 110 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7858 (mmtm) REVERT: H 116 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8137 (mtt) outliers start: 59 outliers final: 29 residues processed: 315 average time/residue: 1.7414 time to fit residues: 630.4907 Evaluate side-chains 330 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 447 ARG Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 447 ARG Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 635 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 166 optimal weight: 4.9990 chunk 170 optimal weight: 0.0570 chunk 16 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 0.0770 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN C 125 ASN C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.100667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.082813 restraints weight = 102083.552| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.63 r_work: 0.2682 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29210 Z= 0.135 Angle : 0.551 7.726 39714 Z= 0.298 Chirality : 0.046 0.174 4022 Planarity : 0.004 0.041 5284 Dihedral : 4.729 23.819 4010 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.83 % Allowed : 9.44 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3550 helix: 1.86 (0.20), residues: 656 sheet: 0.36 (0.20), residues: 740 loop : -0.10 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 22 HIS 0.005 0.001 HIS E 97 PHE 0.013 0.002 PHE E 713 TYR 0.025 0.002 TYR G 661 ARG 0.005 0.000 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1020) hydrogen bonds : angle 4.98265 ( 3352) covalent geometry : bond 0.00303 (29210) covalent geometry : angle 0.55125 (39714) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 3.005 Fit side-chains REVERT: A 445 ASP cc_start: 0.8315 (m-30) cc_final: 0.7964 (m-30) REVERT: A 491 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: A 717 ASN cc_start: 0.8265 (t0) cc_final: 0.7512 (t0) REVERT: A 736 ASN cc_start: 0.8198 (t0) cc_final: 0.7967 (t0) REVERT: B 62 TYR cc_start: 0.8449 (m-80) cc_final: 0.8099 (m-80) REVERT: B 90 TYR cc_start: 0.8924 (m-80) cc_final: 0.8228 (m-80) REVERT: B 110 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7851 (mmtm) REVERT: C 29 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: C 31 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7768 (ttm110) REVERT: C 299 ARG cc_start: 0.8468 (mtp85) cc_final: 0.7805 (tpt170) REVERT: C 737 ASP cc_start: 0.8271 (t0) cc_final: 0.7920 (t70) REVERT: D 60 SER cc_start: 0.8641 (t) cc_final: 0.8352 (p) REVERT: D 78 ARG cc_start: 0.8990 (ptm160) cc_final: 0.8773 (ttm-80) REVERT: D 112 GLU cc_start: 0.7538 (pt0) cc_final: 0.7337 (pt0) REVERT: D 130 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6981 (tp30) REVERT: E 29 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: E 31 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7760 (ttm110) REVERT: E 299 ARG cc_start: 0.8480 (mtp85) cc_final: 0.7814 (tpt170) REVERT: F 60 SER cc_start: 0.8642 (t) cc_final: 0.8360 (p) REVERT: F 78 ARG cc_start: 0.8990 (ptm160) cc_final: 0.8773 (ttm-80) REVERT: F 130 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6969 (tp30) REVERT: G 325 GLU cc_start: 0.8384 (pm20) cc_final: 0.8110 (pm20) REVERT: G 445 ASP cc_start: 0.8311 (m-30) cc_final: 0.7955 (m-30) REVERT: G 491 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: G 717 ASN cc_start: 0.8260 (t0) cc_final: 0.7545 (t0) REVERT: G 736 ASN cc_start: 0.8200 (t0) cc_final: 0.7965 (t0) REVERT: H 62 TYR cc_start: 0.8458 (m-80) cc_final: 0.8116 (m-80) REVERT: H 90 TYR cc_start: 0.8929 (m-80) cc_final: 0.8223 (m-80) REVERT: H 110 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7848 (mmtm) outliers start: 48 outliers final: 24 residues processed: 326 average time/residue: 1.6981 time to fit residues: 634.0128 Evaluate side-chains 317 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 178 optimal weight: 9.9990 chunk 272 optimal weight: 7.9990 chunk 220 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 GLN E 626 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.099316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.081133 restraints weight = 120247.071| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.88 r_work: 0.2667 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2528 r_free = 0.2528 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29210 Z= 0.195 Angle : 0.612 8.163 39714 Z= 0.331 Chirality : 0.048 0.181 4022 Planarity : 0.005 0.044 5284 Dihedral : 4.900 23.959 4010 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.97 % Allowed : 9.61 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3550 helix: 1.75 (0.20), residues: 656 sheet: 0.31 (0.20), residues: 744 loop : -0.15 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 22 HIS 0.007 0.001 HIS E 97 PHE 0.017 0.002 PHE A 187 TYR 0.030 0.002 TYR A 661 ARG 0.006 0.001 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 1020) hydrogen bonds : angle 5.12678 ( 3352) covalent geometry : bond 0.00453 (29210) covalent geometry : angle 0.61234 (39714) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 3.024 Fit side-chains revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8357 (m-30) cc_final: 0.7986 (m-30) REVERT: A 491 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: A 717 ASN cc_start: 0.8273 (t0) cc_final: 0.7989 (t0) REVERT: A 736 ASN cc_start: 0.8209 (t0) cc_final: 0.7964 (t0) REVERT: A 745 MET cc_start: 0.8745 (ttm) cc_final: 0.8531 (ttm) REVERT: B 62 TYR cc_start: 0.8511 (m-80) cc_final: 0.8138 (m-80) REVERT: B 90 TYR cc_start: 0.8939 (m-80) cc_final: 0.8204 (m-80) REVERT: B 110 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7849 (mmtm) REVERT: B 116 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8102 (mtt) REVERT: C 29 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: C 31 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7787 (ttm110) REVERT: C 62 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8251 (tt) REVERT: C 299 ARG cc_start: 0.8495 (mtp85) cc_final: 0.7846 (tpt170) REVERT: C 402 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: C 580 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8774 (mt-10) REVERT: C 737 ASP cc_start: 0.8296 (t0) cc_final: 0.7950 (t70) REVERT: D 60 SER cc_start: 0.8722 (t) cc_final: 0.8436 (p) REVERT: D 78 ARG cc_start: 0.8976 (ptm160) cc_final: 0.8749 (ttm-80) REVERT: D 112 GLU cc_start: 0.7624 (pt0) cc_final: 0.7408 (pt0) REVERT: E 29 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: E 62 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8245 (tt) REVERT: E 299 ARG cc_start: 0.8502 (mtp85) cc_final: 0.7850 (tpt170) REVERT: E 402 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: E 737 ASP cc_start: 0.8296 (t0) cc_final: 0.7966 (t70) REVERT: F 60 SER cc_start: 0.8724 (t) cc_final: 0.8445 (p) REVERT: F 78 ARG cc_start: 0.8973 (ptm160) cc_final: 0.8744 (ttm-80) REVERT: G 445 ASP cc_start: 0.8357 (m-30) cc_final: 0.7982 (m-30) REVERT: G 491 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7988 (mm-30) REVERT: G 717 ASN cc_start: 0.8261 (t0) cc_final: 0.7518 (t0) REVERT: G 736 ASN cc_start: 0.8212 (t0) cc_final: 0.7966 (t0) REVERT: G 745 MET cc_start: 0.8766 (ttm) cc_final: 0.8552 (ttm) REVERT: H 62 TYR cc_start: 0.8518 (m-80) cc_final: 0.8154 (m-80) REVERT: H 90 TYR cc_start: 0.8944 (m-80) cc_final: 0.8202 (m-80) REVERT: H 110 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7845 (mmtm) REVERT: H 116 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8096 (mtt) outliers start: 52 outliers final: 27 residues processed: 313 average time/residue: 1.7226 time to fit residues: 617.9269 Evaluate side-chains 325 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 288 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 337 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 327 optimal weight: 0.0000 chunk 325 optimal weight: 9.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.083061 restraints weight = 114883.073| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.80 r_work: 0.2689 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29210 Z= 0.117 Angle : 0.536 8.460 39714 Z= 0.289 Chirality : 0.045 0.169 4022 Planarity : 0.004 0.041 5284 Dihedral : 4.607 23.769 4010 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.56 % Allowed : 10.32 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3550 helix: 1.93 (0.20), residues: 656 sheet: 0.37 (0.20), residues: 744 loop : -0.07 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 22 HIS 0.005 0.001 HIS C 97 PHE 0.013 0.002 PHE F 120 TYR 0.023 0.001 TYR A 661 ARG 0.005 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1020) hydrogen bonds : angle 4.86060 ( 3352) covalent geometry : bond 0.00261 (29210) covalent geometry : angle 0.53568 (39714) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 3.138 Fit side-chains REVERT: A 445 ASP cc_start: 0.8294 (m-30) cc_final: 0.7911 (m-30) REVERT: A 491 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: A 717 ASN cc_start: 0.8278 (t0) cc_final: 0.7556 (t0) REVERT: A 736 ASN cc_start: 0.8187 (t0) cc_final: 0.7940 (t0) REVERT: B 62 TYR cc_start: 0.8437 (m-80) cc_final: 0.8107 (m-80) REVERT: B 90 TYR cc_start: 0.8934 (m-80) cc_final: 0.8130 (m-80) REVERT: B 110 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7825 (mmtm) REVERT: B 130 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6653 (tm-30) REVERT: C 29 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: C 31 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7827 (ttm110) REVERT: C 299 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7794 (tpt170) REVERT: C 486 ASN cc_start: 0.8790 (m-40) cc_final: 0.8280 (m110) REVERT: C 737 ASP cc_start: 0.8312 (t0) cc_final: 0.7975 (t70) REVERT: D 60 SER cc_start: 0.8606 (t) cc_final: 0.8319 (p) REVERT: D 78 ARG cc_start: 0.8999 (ptm160) cc_final: 0.8757 (ttm-80) REVERT: D 130 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7074 (tp30) REVERT: E 29 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: E 31 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7870 (ttm110) REVERT: E 280 LEU cc_start: 0.8285 (mm) cc_final: 0.8009 (mt) REVERT: E 299 ARG cc_start: 0.8485 (mtp85) cc_final: 0.7802 (tpt170) REVERT: E 486 ASN cc_start: 0.8802 (m-40) cc_final: 0.8295 (m110) REVERT: E 737 ASP cc_start: 0.8310 (t0) cc_final: 0.7977 (t70) REVERT: F 60 SER cc_start: 0.8612 (t) cc_final: 0.8331 (p) REVERT: F 78 ARG cc_start: 0.9001 (ptm160) cc_final: 0.8760 (ttm-80) REVERT: F 130 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7065 (tp30) REVERT: G 325 GLU cc_start: 0.8396 (pm20) cc_final: 0.8128 (pm20) REVERT: G 445 ASP cc_start: 0.8292 (m-30) cc_final: 0.7915 (m-30) REVERT: G 491 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: G 717 ASN cc_start: 0.8278 (t0) cc_final: 0.7558 (t0) REVERT: G 736 ASN cc_start: 0.8175 (t0) cc_final: 0.7929 (t0) REVERT: H 62 TYR cc_start: 0.8457 (m-80) cc_final: 0.8075 (m-80) REVERT: H 90 TYR cc_start: 0.8939 (m-80) cc_final: 0.8137 (m-80) REVERT: H 110 LYS cc_start: 0.8399 (mmmt) cc_final: 0.7823 (mmtm) outliers start: 40 outliers final: 24 residues processed: 325 average time/residue: 1.9455 time to fit residues: 742.9825 Evaluate side-chains 323 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 295 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 279 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 GLN E 626 GLN G 751 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.097731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.079830 restraints weight = 103893.986| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.53 r_work: 0.2642 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 29210 Z= 0.295 Angle : 0.706 9.423 39714 Z= 0.383 Chirality : 0.053 0.194 4022 Planarity : 0.006 0.065 5284 Dihedral : 5.170 24.385 4010 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.80 % Allowed : 10.18 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3550 helix: 1.80 (0.20), residues: 624 sheet: 0.31 (0.19), residues: 760 loop : -0.21 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 473 HIS 0.006 0.002 HIS C 97 PHE 0.021 0.003 PHE A 187 TYR 0.031 0.003 TYR A 661 ARG 0.007 0.001 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.05748 ( 1020) hydrogen bonds : angle 5.33681 ( 3352) covalent geometry : bond 0.00694 (29210) covalent geometry : angle 0.70647 (39714) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 3.803 Fit side-chains REVERT: A 491 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: A 717 ASN cc_start: 0.8309 (t0) cc_final: 0.8041 (t0) REVERT: A 736 ASN cc_start: 0.8288 (t0) cc_final: 0.8055 (t0) REVERT: A 745 MET cc_start: 0.8772 (ttm) cc_final: 0.8472 (ttm) REVERT: B 62 TYR cc_start: 0.8549 (m-80) cc_final: 0.8169 (m-80) REVERT: B 90 TYR cc_start: 0.8947 (m-80) cc_final: 0.8203 (m-80) REVERT: B 110 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7845 (mmtm) REVERT: B 116 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8142 (mtt) REVERT: C 29 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: C 299 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7797 (tpt170) REVERT: C 402 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: D 60 SER cc_start: 0.8763 (t) cc_final: 0.8443 (p) REVERT: D 78 ARG cc_start: 0.8998 (ptm160) cc_final: 0.8719 (ttm-80) REVERT: E 168 GLU cc_start: 0.7780 (pp20) cc_final: 0.7520 (pp20) REVERT: E 299 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7801 (tpt170) REVERT: E 402 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: F 60 SER cc_start: 0.8769 (t) cc_final: 0.8453 (p) REVERT: F 78 ARG cc_start: 0.8999 (ptm160) cc_final: 0.8716 (ttm-80) REVERT: G 491 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: G 717 ASN cc_start: 0.8308 (t0) cc_final: 0.8039 (t0) REVERT: G 736 ASN cc_start: 0.8283 (t0) cc_final: 0.8050 (t0) REVERT: G 745 MET cc_start: 0.8792 (ttm) cc_final: 0.8496 (ttm) REVERT: H 62 TYR cc_start: 0.8559 (m-80) cc_final: 0.8186 (m-80) REVERT: H 90 TYR cc_start: 0.8954 (m-80) cc_final: 0.8207 (m-80) REVERT: H 110 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7839 (mmtm) REVERT: H 116 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8119 (mtt) outliers start: 45 outliers final: 29 residues processed: 312 average time/residue: 1.7340 time to fit residues: 619.4449 Evaluate side-chains 325 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 289 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 116 MET Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 162 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 246 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 GLN E 626 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.099812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.081936 restraints weight = 109503.906| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.72 r_work: 0.2678 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29210 Z= 0.131 Angle : 0.557 9.470 39714 Z= 0.301 Chirality : 0.045 0.169 4022 Planarity : 0.004 0.043 5284 Dihedral : 4.755 23.653 4010 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.32 % Allowed : 10.79 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3550 helix: 1.80 (0.20), residues: 656 sheet: 0.38 (0.20), residues: 736 loop : -0.15 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 22 HIS 0.005 0.001 HIS E 97 PHE 0.013 0.002 PHE E 713 TYR 0.025 0.002 TYR G 661 ARG 0.007 0.000 ARG G 22 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 1020) hydrogen bonds : angle 4.95252 ( 3352) covalent geometry : bond 0.00293 (29210) covalent geometry : angle 0.55742 (39714) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7100 Ramachandran restraints generated. 3550 Oldfield, 0 Emsley, 3550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 295 time to evaluate : 2.983 Fit side-chains revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8110 (mppt) cc_final: 0.7751 (mptm) REVERT: A 445 ASP cc_start: 0.8324 (m-30) cc_final: 0.7918 (m-30) REVERT: A 491 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: A 717 ASN cc_start: 0.8267 (t0) cc_final: 0.7524 (t0) REVERT: A 736 ASN cc_start: 0.8188 (t0) cc_final: 0.7959 (t0) REVERT: B 62 TYR cc_start: 0.8459 (m-80) cc_final: 0.8099 (m-80) REVERT: B 90 TYR cc_start: 0.8942 (m-80) cc_final: 0.8251 (m-80) REVERT: B 110 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8112 (mmmt) REVERT: B 130 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6805 (mt-10) REVERT: C 29 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: C 299 ARG cc_start: 0.8476 (mtp85) cc_final: 0.7795 (tpt170) REVERT: C 402 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: C 737 ASP cc_start: 0.8321 (t0) cc_final: 0.7987 (t70) REVERT: D 60 SER cc_start: 0.8640 (t) cc_final: 0.8345 (p) REVERT: D 78 ARG cc_start: 0.9019 (ptm160) cc_final: 0.8766 (ttm-80) REVERT: D 130 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7166 (tp30) REVERT: E 29 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: E 31 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7839 (ttm110) REVERT: E 168 GLU cc_start: 0.7838 (pp20) cc_final: 0.7633 (pp20) REVERT: E 299 ARG cc_start: 0.8489 (mtp85) cc_final: 0.7807 (tpt170) REVERT: E 402 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: E 737 ASP cc_start: 0.8316 (t0) cc_final: 0.7991 (t70) REVERT: F 60 SER cc_start: 0.8623 (t) cc_final: 0.8346 (p) REVERT: F 78 ARG cc_start: 0.9022 (ptm160) cc_final: 0.8767 (ttm-80) REVERT: F 130 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7169 (tp30) REVERT: G 59 LYS cc_start: 0.8112 (mppt) cc_final: 0.7761 (mptm) REVERT: G 445 ASP cc_start: 0.8317 (m-30) cc_final: 0.7906 (m-30) REVERT: G 491 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7952 (mm-30) REVERT: G 717 ASN cc_start: 0.8261 (t0) cc_final: 0.7552 (t0) REVERT: G 736 ASN cc_start: 0.8182 (t0) cc_final: 0.7950 (t0) REVERT: H 62 TYR cc_start: 0.8459 (m-80) cc_final: 0.8117 (m-80) REVERT: H 90 TYR cc_start: 0.8945 (m-80) cc_final: 0.8250 (m-80) REVERT: H 110 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8115 (mmmt) outliers start: 31 outliers final: 23 residues processed: 310 average time/residue: 1.7255 time to fit residues: 616.2045 Evaluate side-chains 322 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 293 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 628 GLU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 628 GLU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 279 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 314 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 626 GLN E 626 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.080635 restraints weight = 99382.547| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.43 r_work: 0.2656 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 29210 Z= 0.259 Angle : 0.677 9.276 39714 Z= 0.367 Chirality : 0.051 0.188 4022 Planarity : 0.006 0.059 5284 Dihedral : 5.099 24.100 4010 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.90 % Allowed : 10.18 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3550 helix: 1.84 (0.20), residues: 624 sheet: 0.31 (0.19), residues: 760 loop : -0.20 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 473 HIS 0.006 0.002 HIS D 48 PHE 0.020 0.003 PHE A 187 TYR 0.031 0.002 TYR A 661 ARG 0.006 0.001 ARG G 299 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 1020) hydrogen bonds : angle 5.26653 ( 3352) covalent geometry : bond 0.00608 (29210) covalent geometry : angle 0.67730 (39714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22370.89 seconds wall clock time: 384 minutes 33.78 seconds (23073.78 seconds total)