Starting phenix.real_space_refine on Fri Mar 6 05:33:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w8j_32357/03_2026/7w8j_32357.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w8j_32357/03_2026/7w8j_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_32357/03_2026/7w8j_32357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w8j_32357/03_2026/7w8j_32357.map" model { file = "/net/cci-nas-00/data/ceres_data/7w8j_32357/03_2026/7w8j_32357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w8j_32357/03_2026/7w8j_32357.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 10.98, per 1000 atoms: 0.38 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: 1.96 Conformation dependent library (CDL) restraints added in 2.0 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: 1.63 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: 7.99 Time building geometry restraints manager: 2.73 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: 0.03 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 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 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 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 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.730 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.030 0.001 ARG A 22 TYR 0.037 0.003 TYR D 90 PHE 0.033 0.002 PHE F 53 TRP 0.017 0.002 TRP F 22 HIS 0.019 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.01362 (29210) covalent geometry : angle 1.61564 (39714) hydrogen bonds : bond 0.18366 ( 1020) hydrogen bonds : angle 7.32139 ( 3352) *********************** 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 : 1.081 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: 0.7813 (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: 0.7318 (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: 0.6544 (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: 0.9184 time to fit residues: 420.1890 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 : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.102245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.085285 restraints weight = 97773.689| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.49 r_work: 0.2725 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29210 Z= 0.132 Angle : 0.567 7.499 39714 Z= 0.310 Chirality : 0.045 0.180 4022 Planarity : 0.004 0.033 5284 Dihedral : 4.593 25.364 4010 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.19 % Allowed : 6.82 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3550 helix: 1.88 (0.20), residues: 672 sheet: 0.20 (0.19), residues: 756 loop : -0.05 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 462 TYR 0.029 0.002 TYR A 661 PHE 0.016 0.002 PHE H 120 TRP 0.017 0.002 TRP D 22 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00281 (29210) covalent geometry : angle 0.56696 (39714) hydrogen bonds : bond 0.04720 ( 1020) hydrogen bonds : angle 5.24204 ( 3352) *********************** 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 357 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 326 time to evaluate : 1.085 Fit side-chains REVERT: A 445 ASP cc_start: 0.8169 (m-30) cc_final: 0.7959 (m-30) REVERT: A 491 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: A 497 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 537 ASP cc_start: 0.8024 (p0) cc_final: 0.7806 (m-30) REVERT: A 717 ASN cc_start: 0.8030 (t0) cc_final: 0.7363 (t0) REVERT: A 736 ASN cc_start: 0.8184 (t0) cc_final: 0.7946 (t0) REVERT: A 745 MET cc_start: 0.8901 (ttm) cc_final: 0.8640 (ttm) REVERT: B 11 ASP cc_start: 0.8091 (t0) cc_final: 0.7767 (t70) REVERT: B 14 ASN cc_start: 0.8563 (m-40) cc_final: 0.8348 (m-40) REVERT: B 62 TYR cc_start: 0.8443 (m-80) cc_final: 0.8110 (m-80) REVERT: B 90 TYR cc_start: 0.8871 (m-80) cc_final: 0.8298 (m-80) REVERT: B 110 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8058 (mptm) REVERT: C 168 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7476 (tp30) REVERT: C 264 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7919 (mtt180) REVERT: C 299 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7806 (tpt170) REVERT: C 737 ASP cc_start: 0.8175 (t0) cc_final: 0.7724 (t70) REVERT: D 27 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: D 40 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: D 51 ASN cc_start: 0.7872 (t0) cc_final: 0.7563 (t0) REVERT: E 168 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7493 (tp30) REVERT: E 211 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8349 (mt-10) REVERT: E 264 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7915 (mtt180) REVERT: E 299 ARG cc_start: 0.8413 (mtp85) cc_final: 0.7815 (tpt170) REVERT: E 737 ASP cc_start: 0.8173 (t0) cc_final: 0.7721 (t70) REVERT: F 27 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: F 51 ASN cc_start: 0.7880 (t0) cc_final: 0.7593 (t0) REVERT: G 445 ASP cc_start: 0.8155 (m-30) cc_final: 0.7951 (m-30) REVERT: G 491 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: G 497 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8159 (mt-10) REVERT: G 537 ASP cc_start: 0.8035 (p0) cc_final: 0.7812 (m-30) REVERT: G 717 ASN cc_start: 0.8038 (t0) cc_final: 0.7362 (t0) REVERT: G 736 ASN cc_start: 0.8176 (t0) cc_final: 0.7932 (t0) REVERT: G 745 MET cc_start: 0.8909 (ttm) cc_final: 0.8652 (ttm) REVERT: H 11 ASP cc_start: 0.8098 (t0) cc_final: 0.7765 (t70) REVERT: H 14 ASN cc_start: 0.8556 (m-40) cc_final: 0.8343 (m-40) REVERT: H 62 TYR cc_start: 0.8444 (m-80) cc_final: 0.8115 (m-80) REVERT: H 90 TYR cc_start: 0.8873 (m-80) cc_final: 0.8308 (m-80) REVERT: H 110 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8069 (mptm) outliers start: 31 outliers final: 14 residues processed: 343 average time/residue: 0.8518 time to fit residues: 332.4726 Evaluate side-chains 313 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 294 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 C residue 382 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 27 ASP 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 280 LEU 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 76 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 246 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 108 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 339 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 HIS E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3106 r_free = 0.3106 target = 0.098560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.080489 restraints weight = 118721.887| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.84 r_work: 0.2656 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29210 Z= 0.199 Angle : 0.621 8.127 39714 Z= 0.338 Chirality : 0.049 0.189 4022 Planarity : 0.005 0.043 5284 Dihedral : 4.861 24.906 4010 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.80 % Allowed : 8.18 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3550 helix: 1.80 (0.20), residues: 676 sheet: 0.28 (0.19), residues: 756 loop : -0.06 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 22 TYR 0.030 0.002 TYR G 661 PHE 0.016 0.002 PHE G 187 TRP 0.013 0.002 TRP D 22 HIS 0.007 0.002 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00467 (29210) covalent geometry : angle 0.62127 (39714) hydrogen bonds : bond 0.05259 ( 1020) hydrogen bonds : angle 5.23477 ( 3352) *********************** 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 353 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 1.242 Fit side-chains REVERT: A 445 ASP cc_start: 0.8366 (m-30) cc_final: 0.8061 (m-30) REVERT: A 491 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: A 506 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7804 (tp30) REVERT: A 717 ASN cc_start: 0.8228 (t0) cc_final: 0.7453 (t0) REVERT: A 736 ASN cc_start: 0.8259 (t0) cc_final: 0.8010 (t0) REVERT: B 32 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8218 (mtpm) REVERT: B 62 TYR cc_start: 0.8515 (m-80) cc_final: 0.8199 (m-80) REVERT: B 90 TYR cc_start: 0.8918 (m-80) cc_final: 0.8376 (m-80) REVERT: B 110 LYS cc_start: 0.8472 (mmmt) cc_final: 0.7920 (mmtm) REVERT: C 31 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7831 (ttp80) REVERT: C 299 ARG cc_start: 0.8463 (mtp85) cc_final: 0.7838 (tpt170) REVERT: C 737 ASP cc_start: 0.8217 (t0) cc_final: 0.7828 (t70) REVERT: D 32 LYS cc_start: 0.8578 (mttm) cc_final: 0.8358 (mttm) REVERT: D 88 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7892 (t70) REVERT: D 130 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6951 (tp30) REVERT: E 31 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7816 (ttp80) REVERT: E 299 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7845 (tpt170) REVERT: E 737 ASP cc_start: 0.8217 (t0) cc_final: 0.7823 (t70) REVERT: F 32 LYS cc_start: 0.8564 (mttm) cc_final: 0.8352 (mttm) REVERT: F 88 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7891 (t70) REVERT: F 130 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6947 (tp30) REVERT: G 425 ASP cc_start: 0.8041 (m-30) cc_final: 0.7826 (m-30) REVERT: G 445 ASP cc_start: 0.8342 (m-30) cc_final: 0.8043 (m-30) REVERT: G 491 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: G 506 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: G 717 ASN cc_start: 0.8218 (t0) cc_final: 0.7446 (t0) REVERT: G 736 ASN cc_start: 0.8249 (t0) cc_final: 0.8000 (t0) REVERT: H 32 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8219 (mtpm) REVERT: H 62 TYR cc_start: 0.8522 (m-80) cc_final: 0.8210 (m-80) REVERT: H 90 TYR cc_start: 0.8924 (m-80) cc_final: 0.8306 (m-80) REVERT: H 110 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7879 (mmtm) outliers start: 49 outliers final: 22 residues processed: 324 average time/residue: 0.8497 time to fit residues: 313.8600 Evaluate side-chains 319 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 60 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 88 ASP Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 61 ASP 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 337 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 177 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** 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 = 0.3107 r_free = 0.3107 target = 0.098876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.080845 restraints weight = 105727.336| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.72 r_work: 0.2647 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 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 = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29210 Z= 0.215 Angle : 0.635 8.007 39714 Z= 0.345 Chirality : 0.049 0.186 4022 Planarity : 0.005 0.047 5284 Dihedral : 4.993 24.621 4010 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.07 % Allowed : 9.03 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3550 helix: 1.56 (0.19), residues: 680 sheet: 0.23 (0.19), residues: 756 loop : -0.15 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 78 TYR 0.031 0.002 TYR G 661 PHE 0.017 0.002 PHE A 187 TRP 0.016 0.002 TRP C 473 HIS 0.007 0.002 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00500 (29210) covalent geometry : angle 0.63479 (39714) hydrogen bonds : bond 0.05252 ( 1020) hydrogen bonds : angle 5.24804 ( 3352) *********************** 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 353 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 298 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8375 (m-30) cc_final: 0.7992 (m-30) REVERT: A 491 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8000 (mm-30) REVERT: A 717 ASN cc_start: 0.8265 (t0) cc_final: 0.8014 (t0) REVERT: A 736 ASN cc_start: 0.8260 (t0) cc_final: 0.8021 (t0) REVERT: A 745 MET cc_start: 0.8805 (ttm) cc_final: 0.8526 (ttm) REVERT: B 62 TYR cc_start: 0.8567 (m-80) cc_final: 0.8207 (m-80) REVERT: B 90 TYR cc_start: 0.8933 (m-80) cc_final: 0.8299 (m-80) REVERT: B 110 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8127 (mmmt) REVERT: B 116 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8139 (mtt) REVERT: C 62 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8206 (tt) REVERT: C 299 ARG cc_start: 0.8474 (mtp85) cc_final: 0.7835 (tpt170) REVERT: C 737 ASP cc_start: 0.8320 (t0) cc_final: 0.7955 (t70) REVERT: D 32 LYS cc_start: 0.8522 (mttm) cc_final: 0.8235 (mttm) REVERT: D 88 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7931 (t70) REVERT: E 62 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8206 (tt) REVERT: E 168 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7532 (tm-30) REVERT: E 211 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8476 (mt-10) REVERT: E 299 ARG cc_start: 0.8482 (mtp85) cc_final: 0.7838 (tpt170) REVERT: E 737 ASP cc_start: 0.8320 (t0) cc_final: 0.7951 (t70) REVERT: F 32 LYS cc_start: 0.8531 (mttm) cc_final: 0.8249 (mttm) REVERT: F 112 GLU cc_start: 0.7667 (pt0) cc_final: 0.7439 (pt0) REVERT: G 425 ASP cc_start: 0.8051 (m-30) cc_final: 0.7836 (m-30) REVERT: G 445 ASP cc_start: 0.8373 (m-30) cc_final: 0.7988 (m-30) REVERT: G 491 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7998 (mm-30) REVERT: G 717 ASN cc_start: 0.8260 (t0) cc_final: 0.7556 (t0) REVERT: G 736 ASN cc_start: 0.8275 (t0) cc_final: 0.8038 (t0) REVERT: G 745 MET cc_start: 0.8821 (ttm) cc_final: 0.8543 (ttm) REVERT: H 62 TYR cc_start: 0.8568 (m-80) cc_final: 0.8211 (m-80) REVERT: H 90 TYR cc_start: 0.8933 (m-80) cc_final: 0.8300 (m-80) REVERT: H 110 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8122 (mmmt) REVERT: H 116 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8144 (mtt) outliers start: 55 outliers final: 20 residues processed: 320 average time/residue: 0.8382 time to fit residues: 305.6958 Evaluate side-chains 321 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 294 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 116 MET Chi-restraints excluded: chain C residue 62 LEU 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 D residue 88 ASP Chi-restraints excluded: chain E residue 62 LEU 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 280 LEU Chi-restraints excluded: chain G residue 491 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 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 253 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 412 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.081516 restraints weight = 103896.443| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.71 r_work: 0.2685 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29210 Z= 0.145 Angle : 0.565 7.831 39714 Z= 0.306 Chirality : 0.046 0.175 4022 Planarity : 0.004 0.040 5284 Dihedral : 4.778 23.940 4010 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.80 % Allowed : 9.64 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3550 helix: 1.86 (0.20), residues: 656 sheet: 0.37 (0.20), residues: 740 loop : -0.09 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.026 0.002 TYR G 661 PHE 0.014 0.002 PHE E 713 TRP 0.015 0.002 TRP E 473 HIS 0.006 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00329 (29210) covalent geometry : angle 0.56457 (39714) hydrogen bonds : bond 0.04580 ( 1020) hydrogen bonds : angle 5.03911 ( 3352) *********************** 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: 47 poor density : 307 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 GLU cc_start: 0.8371 (pm20) cc_final: 0.8100 (pm20) REVERT: A 445 ASP cc_start: 0.8332 (m-30) cc_final: 0.7983 (m-30) REVERT: A 491 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (mm-30) REVERT: A 717 ASN cc_start: 0.8220 (t0) cc_final: 0.7456 (t0) REVERT: A 736 ASN cc_start: 0.8206 (t0) cc_final: 0.7984 (t0) REVERT: B 62 TYR cc_start: 0.8457 (m-80) cc_final: 0.8113 (m-80) REVERT: B 90 TYR cc_start: 0.8937 (m-80) cc_final: 0.8183 (m-80) REVERT: B 110 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8110 (mmmt) REVERT: C 196 ASP cc_start: 0.8523 (m-30) cc_final: 0.8315 (m-30) REVERT: C 299 ARG cc_start: 0.8484 (mtp85) cc_final: 0.7820 (tpt170) REVERT: C 737 ASP cc_start: 0.8300 (t0) cc_final: 0.7941 (t70) REVERT: D 32 LYS cc_start: 0.8532 (mttm) cc_final: 0.8256 (mttm) REVERT: D 88 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7890 (t70) REVERT: D 130 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7031 (tp30) REVERT: E 211 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8473 (mt-10) REVERT: E 299 ARG cc_start: 0.8491 (mtp85) cc_final: 0.7826 (tpt170) REVERT: E 737 ASP cc_start: 0.8305 (t0) cc_final: 0.7943 (t70) REVERT: F 32 LYS cc_start: 0.8537 (mttm) cc_final: 0.8250 (mttm) REVERT: F 130 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7020 (tp30) REVERT: G 445 ASP cc_start: 0.8331 (m-30) cc_final: 0.7985 (m-30) REVERT: G 491 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: G 717 ASN cc_start: 0.8230 (t0) cc_final: 0.7473 (t0) REVERT: G 736 ASN cc_start: 0.8213 (t0) cc_final: 0.7966 (t0) REVERT: H 62 TYR cc_start: 0.8463 (m-80) cc_final: 0.8121 (m-80) REVERT: H 90 TYR cc_start: 0.8953 (m-80) cc_final: 0.8202 (m-80) REVERT: H 110 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8099 (mmmt) outliers start: 47 outliers final: 24 residues processed: 328 average time/residue: 0.7990 time to fit residues: 300.0667 Evaluate side-chains 318 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 291 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 141 SER Chi-restraints excluded: chain A residue 491 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 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 D residue 60 SER Chi-restraints excluded: chain D residue 88 ASP 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 F residue 60 SER Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 491 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 170 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 324 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 751 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.098293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.080748 restraints weight = 96513.894| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.38 r_work: 0.2658 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2531 r_free = 0.2531 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 29210 Z= 0.270 Angle : 0.682 7.715 39714 Z= 0.371 Chirality : 0.052 0.191 4022 Planarity : 0.006 0.059 5284 Dihedral : 5.145 24.173 4010 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.97 % Allowed : 9.84 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3550 helix: 1.79 (0.20), residues: 624 sheet: 0.31 (0.20), residues: 736 loop : -0.22 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 78 TYR 0.030 0.003 TYR A 661 PHE 0.020 0.003 PHE A 187 TRP 0.015 0.002 TRP C 473 HIS 0.008 0.002 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00634 (29210) covalent geometry : angle 0.68229 (39714) hydrogen bonds : bond 0.05646 ( 1020) hydrogen bonds : angle 5.33829 ( 3352) *********************** 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 351 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 299 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: A 717 ASN cc_start: 0.8304 (t0) cc_final: 0.8034 (t0) REVERT: A 736 ASN cc_start: 0.8262 (t0) cc_final: 0.8020 (t0) REVERT: A 745 MET cc_start: 0.8812 (ttm) cc_final: 0.8543 (ttm) REVERT: B 62 TYR cc_start: 0.8537 (m-80) cc_final: 0.8191 (m-80) REVERT: B 90 TYR cc_start: 0.8948 (m-80) cc_final: 0.8212 (m-80) REVERT: B 110 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7864 (mmtm) REVERT: B 116 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8087 (mtt) REVERT: C 62 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8286 (tt) REVERT: C 196 ASP cc_start: 0.8546 (m-30) cc_final: 0.8338 (m-30) REVERT: C 299 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7837 (tpt170) REVERT: C 737 ASP cc_start: 0.8247 (t0) cc_final: 0.7900 (t70) REVERT: E 62 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8287 (tt) REVERT: E 299 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7832 (tpt170) REVERT: E 737 ASP cc_start: 0.8261 (t0) cc_final: 0.7911 (t70) REVERT: G 491 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: G 717 ASN cc_start: 0.8301 (t0) cc_final: 0.8031 (t0) REVERT: G 736 ASN cc_start: 0.8273 (t0) cc_final: 0.8036 (t0) REVERT: G 745 MET cc_start: 0.8824 (ttm) cc_final: 0.8555 (ttm) REVERT: H 62 TYR cc_start: 0.8540 (m-80) cc_final: 0.8194 (m-80) REVERT: H 90 TYR cc_start: 0.8954 (m-80) cc_final: 0.8211 (m-80) REVERT: H 110 LYS cc_start: 0.8416 (mmmt) cc_final: 0.7854 (mmtm) REVERT: H 116 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8094 (mtt) outliers start: 52 outliers final: 25 residues processed: 323 average time/residue: 0.8259 time to fit residues: 304.5291 Evaluate side-chains 323 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 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 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 111 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 298 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 62 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 184 optimal weight: 0.0870 chunk 346 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 GLN C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 412 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.083385 restraints weight = 103869.196| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.60 r_work: 0.2699 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29210 Z= 0.129 Angle : 0.551 7.544 39714 Z= 0.298 Chirality : 0.045 0.171 4022 Planarity : 0.004 0.043 5284 Dihedral : 4.728 23.717 4010 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.70 % Allowed : 10.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3550 helix: 1.79 (0.20), residues: 656 sheet: 0.40 (0.20), residues: 732 loop : -0.14 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.024 0.001 TYR A 661 PHE 0.013 0.002 PHE E 713 TRP 0.015 0.001 TRP C 473 HIS 0.005 0.001 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00288 (29210) covalent geometry : angle 0.55074 (39714) hydrogen bonds : bond 0.04296 ( 1020) hydrogen bonds : angle 4.95358 ( 3352) *********************** 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 346 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8295 (m-30) cc_final: 0.7929 (m-30) REVERT: A 447 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8184 (tmm-80) REVERT: A 491 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: A 717 ASN cc_start: 0.8279 (t0) cc_final: 0.7550 (t0) REVERT: A 736 ASN cc_start: 0.8194 (t0) cc_final: 0.7959 (t0) REVERT: B 62 TYR cc_start: 0.8455 (m-80) cc_final: 0.8107 (m-80) REVERT: B 90 TYR cc_start: 0.8917 (m-80) cc_final: 0.8125 (m-80) REVERT: B 110 LYS cc_start: 0.8388 (mmmt) cc_final: 0.7826 (mmtm) REVERT: C 62 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8200 (tt) REVERT: C 196 ASP cc_start: 0.8500 (m-30) cc_final: 0.8291 (m-30) REVERT: C 299 ARG cc_start: 0.8485 (mtp85) cc_final: 0.7817 (tpt170) REVERT: C 402 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: C 737 ASP cc_start: 0.8271 (t0) cc_final: 0.7925 (t70) REVERT: D 60 SER cc_start: 0.8603 (t) cc_final: 0.8322 (p) REVERT: D 130 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7106 (tp30) REVERT: E 62 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8193 (tt) REVERT: E 299 ARG cc_start: 0.8488 (mtp85) cc_final: 0.7823 (tpt170) REVERT: E 402 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: E 737 ASP cc_start: 0.8276 (t0) cc_final: 0.7932 (t70) REVERT: F 60 SER cc_start: 0.8607 (t) cc_final: 0.8332 (p) REVERT: F 130 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7082 (tp30) REVERT: G 445 ASP cc_start: 0.8282 (m-30) cc_final: 0.7908 (m-30) REVERT: G 447 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8180 (tmm-80) REVERT: G 491 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: G 717 ASN cc_start: 0.8264 (t0) cc_final: 0.7539 (t0) REVERT: G 736 ASN cc_start: 0.8200 (t0) cc_final: 0.7971 (t0) REVERT: H 62 TYR cc_start: 0.8456 (m-80) cc_final: 0.8107 (m-80) REVERT: H 90 TYR cc_start: 0.8923 (m-80) cc_final: 0.8133 (m-80) REVERT: H 110 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7818 (mmtm) outliers start: 42 outliers final: 20 residues processed: 330 average time/residue: 0.8499 time to fit residues: 319.4790 Evaluate side-chains 324 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 296 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 C residue 62 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 402 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 E residue 62 LEU Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 402 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 280 LEU Chi-restraints excluded: chain G residue 447 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 132 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 345 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 205 optimal weight: 0.0370 chunk 171 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 overall best weight: 4.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.098839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.080625 restraints weight = 112653.704| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.73 r_work: 0.2656 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- 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 = 0.18 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: 0.8746 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29210 Z= 0.230 Angle : 0.642 7.801 39714 Z= 0.348 Chirality : 0.050 0.185 4022 Planarity : 0.005 0.052 5284 Dihedral : 5.015 24.053 4010 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.07 % Allowed : 10.35 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3550 helix: 1.90 (0.20), residues: 624 sheet: 0.33 (0.20), residues: 716 loop : -0.17 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 78 TYR 0.032 0.002 TYR G 661 PHE 0.018 0.003 PHE A 187 TRP 0.014 0.002 TRP C 473 HIS 0.006 0.002 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00538 (29210) covalent geometry : angle 0.64198 (39714) hydrogen bonds : bond 0.05263 ( 1020) hydrogen bonds : angle 5.20653 ( 3352) *********************** 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 348 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 297 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 445 ASP cc_start: 0.8330 (m-30) cc_final: 0.7999 (m-30) REVERT: A 447 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8309 (tmm-80) REVERT: A 491 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8001 (mm-30) REVERT: A 717 ASN cc_start: 0.8298 (t0) cc_final: 0.8016 (t0) REVERT: A 736 ASN cc_start: 0.8243 (t0) cc_final: 0.8027 (t0) REVERT: A 745 MET cc_start: 0.8808 (ttm) cc_final: 0.8536 (ttm) REVERT: B 62 TYR cc_start: 0.8537 (m-80) cc_final: 0.8162 (m-80) REVERT: B 90 TYR cc_start: 0.8945 (m-80) cc_final: 0.8195 (m-80) REVERT: B 110 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7862 (mmtm) REVERT: B 116 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8112 (mtt) REVERT: B 130 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 31 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7690 (ttm110) REVERT: C 62 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8304 (tt) REVERT: C 196 ASP cc_start: 0.8554 (m-30) cc_final: 0.8328 (m-30) REVERT: C 299 ARG cc_start: 0.8498 (mtp85) cc_final: 0.7836 (tpt170) REVERT: C 402 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: C 580 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8764 (mt-10) REVERT: C 737 ASP cc_start: 0.8255 (t0) cc_final: 0.7934 (t70) REVERT: D 130 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7091 (tp30) REVERT: E 31 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7687 (ttm110) REVERT: E 62 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (tt) REVERT: E 299 ARG cc_start: 0.8498 (mtp85) cc_final: 0.7839 (tpt170) REVERT: E 402 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: E 737 ASP cc_start: 0.8259 (t0) cc_final: 0.7932 (t70) REVERT: F 130 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7086 (tp30) REVERT: G 445 ASP cc_start: 0.8324 (m-30) cc_final: 0.7984 (m-30) REVERT: G 447 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8306 (tmm-80) REVERT: G 491 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: G 717 ASN cc_start: 0.8286 (t0) cc_final: 0.8006 (t0) REVERT: G 736 ASN cc_start: 0.8244 (t0) cc_final: 0.7998 (t0) REVERT: G 745 MET cc_start: 0.8822 (ttm) cc_final: 0.8550 (ttm) REVERT: H 62 TYR cc_start: 0.8540 (m-80) cc_final: 0.8167 (m-80) REVERT: H 90 TYR cc_start: 0.8948 (m-80) cc_final: 0.8191 (m-80) REVERT: H 110 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7850 (mmtm) REVERT: H 116 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8114 (mtt) REVERT: H 130 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6727 (tm-30) outliers start: 51 outliers final: 28 residues processed: 325 average time/residue: 0.8753 time to fit residues: 323.1010 Evaluate side-chains 338 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 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 116 MET Chi-restraints excluded: chain C residue 1 MET 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 78 ARG Chi-restraints excluded: chain D residue 111 THR 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 27 ASP Chi-restraints excluded: chain F residue 78 ARG 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 447 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 157 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 238 optimal weight: 0.0020 chunk 203 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.084044 restraints weight = 113884.332| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.75 r_work: 0.2736 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2309 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= 0.099 Angle : 0.514 8.582 39714 Z= 0.277 Chirality : 0.044 0.174 4022 Planarity : 0.004 0.044 5284 Dihedral : 4.504 23.826 4010 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.09 % Allowed : 11.34 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3550 helix: 1.94 (0.20), residues: 656 sheet: 0.52 (0.20), residues: 712 loop : -0.07 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 22 TYR 0.020 0.001 TYR C 661 PHE 0.015 0.002 PHE F 120 TRP 0.020 0.001 TRP A 525 HIS 0.004 0.001 HIS G 234 Details of bonding type rmsd covalent geometry : bond 0.00213 (29210) covalent geometry : angle 0.51403 (39714) hydrogen bonds : bond 0.03723 ( 1020) hydrogen bonds : angle 4.76302 ( 3352) *********************** 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 340 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 1.132 Fit side-chains REVERT: A 299 ARG cc_start: 0.8409 (ttp80) cc_final: 0.8203 (ttp80) REVERT: A 409 ASP cc_start: 0.7489 (m-30) cc_final: 0.7201 (m-30) REVERT: A 445 ASP cc_start: 0.8238 (m-30) cc_final: 0.7924 (m-30) REVERT: A 491 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: A 506 GLU cc_start: 0.8420 (tt0) cc_final: 0.7822 (tp30) REVERT: A 717 ASN cc_start: 0.8214 (t0) cc_final: 0.7496 (t0) REVERT: A 736 ASN cc_start: 0.8114 (t0) cc_final: 0.7872 (t0) REVERT: B 62 TYR cc_start: 0.8363 (m-80) cc_final: 0.8033 (m-80) REVERT: B 90 TYR cc_start: 0.8940 (m-80) cc_final: 0.8228 (m-80) REVERT: B 110 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7842 (mmtm) REVERT: B 130 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6690 (tm-30) REVERT: C 196 ASP cc_start: 0.8487 (m-30) cc_final: 0.8279 (m-30) REVERT: C 299 ARG cc_start: 0.8508 (mtp85) cc_final: 0.7822 (tpt170) REVERT: C 486 ASN cc_start: 0.8753 (m-40) cc_final: 0.8261 (m110) REVERT: C 737 ASP cc_start: 0.8264 (t0) cc_final: 0.7915 (t70) REVERT: D 60 SER cc_start: 0.8535 (t) cc_final: 0.8280 (p) REVERT: E 31 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7839 (ttp80) REVERT: E 299 ARG cc_start: 0.8511 (mtp85) cc_final: 0.7832 (tpt170) REVERT: E 486 ASN cc_start: 0.8760 (m-40) cc_final: 0.8266 (m110) REVERT: E 737 ASP cc_start: 0.8266 (t0) cc_final: 0.7913 (t70) REVERT: F 60 SER cc_start: 0.8539 (t) cc_final: 0.8287 (p) REVERT: F 110 LYS cc_start: 0.8637 (mtpp) cc_final: 0.8149 (mttp) REVERT: G 409 ASP cc_start: 0.7473 (m-30) cc_final: 0.7186 (m-30) REVERT: G 445 ASP cc_start: 0.8239 (m-30) cc_final: 0.7917 (m-30) REVERT: G 491 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: G 506 GLU cc_start: 0.8401 (tt0) cc_final: 0.7804 (tp30) REVERT: G 717 ASN cc_start: 0.8215 (t0) cc_final: 0.7498 (t0) REVERT: G 736 ASN cc_start: 0.8105 (t0) cc_final: 0.7861 (t0) REVERT: H 62 TYR cc_start: 0.8376 (m-80) cc_final: 0.8049 (m-80) REVERT: H 90 TYR cc_start: 0.8942 (m-80) cc_final: 0.8226 (m-80) REVERT: H 110 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7835 (mmtm) REVERT: H 130 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6681 (tm-30) outliers start: 22 outliers final: 13 residues processed: 331 average time/residue: 0.8437 time to fit residues: 318.8521 Evaluate side-chains 308 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 293 time to evaluate : 1.297 ------------------------------------------------------------------------------- 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 35 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain F residue 8 CYS 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 35 ILE Chi-restraints excluded: chain H residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 347 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 153 optimal weight: 0.3980 chunk 131 optimal weight: 7.9990 chunk 311 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 740 ASN C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN ** E 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.099623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.081474 restraints weight = 112432.833| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.74 r_work: 0.2668 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 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 = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29210 Z= 0.188 Angle : 0.603 8.201 39714 Z= 0.326 Chirality : 0.048 0.177 4022 Planarity : 0.005 0.042 5284 Dihedral : 4.835 23.787 4010 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.19 % Allowed : 11.30 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3550 helix: 1.87 (0.20), residues: 656 sheet: 0.40 (0.20), residues: 716 loop : -0.11 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 22 TYR 0.029 0.002 TYR G 661 PHE 0.017 0.002 PHE A 187 TRP 0.014 0.002 TRP C 473 HIS 0.007 0.001 HIS C 97 Details of bonding type rmsd covalent geometry : bond 0.00437 (29210) covalent geometry : angle 0.60255 (39714) hydrogen bonds : bond 0.04837 ( 1020) hydrogen bonds : angle 5.05307 ( 3352) ********************** 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 323 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 1.081 Fit side-chains REVERT: A 445 ASP cc_start: 0.8366 (m-30) cc_final: 0.7996 (m-30) REVERT: A 491 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: A 506 GLU cc_start: 0.8483 (tt0) cc_final: 0.7875 (tp30) REVERT: A 717 ASN cc_start: 0.8269 (t0) cc_final: 0.7569 (t0) REVERT: A 736 ASN cc_start: 0.8186 (t0) cc_final: 0.7972 (t0) REVERT: B 62 TYR cc_start: 0.8489 (m-80) cc_final: 0.8137 (m-80) REVERT: B 90 TYR cc_start: 0.8951 (m-80) cc_final: 0.8196 (m-80) REVERT: B 110 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7842 (mmtm) REVERT: C 196 ASP cc_start: 0.8513 (m-30) cc_final: 0.8296 (m-30) REVERT: C 299 ARG cc_start: 0.8502 (mtp85) cc_final: 0.7849 (tpt170) REVERT: C 402 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: C 737 ASP cc_start: 0.8251 (t0) cc_final: 0.7905 (t70) REVERT: D 130 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7122 (tp30) REVERT: E 31 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7686 (ttm110) REVERT: E 168 GLU cc_start: 0.7618 (pp20) cc_final: 0.7336 (pp20) REVERT: E 299 ARG cc_start: 0.8506 (mtp85) cc_final: 0.7850 (tpt170) REVERT: E 402 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: E 447 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8150 (tmm-80) REVERT: E 737 ASP cc_start: 0.8249 (t0) cc_final: 0.7898 (t70) REVERT: F 130 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7115 (tp30) REVERT: G 445 ASP cc_start: 0.8352 (m-30) cc_final: 0.7976 (m-30) REVERT: G 491 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: G 506 GLU cc_start: 0.8487 (tt0) cc_final: 0.7880 (tp30) REVERT: G 717 ASN cc_start: 0.8239 (t0) cc_final: 0.7540 (t0) REVERT: G 736 ASN cc_start: 0.8178 (t0) cc_final: 0.7963 (t0) REVERT: H 62 TYR cc_start: 0.8493 (m-80) cc_final: 0.8144 (m-80) REVERT: H 90 TYR cc_start: 0.8950 (m-80) cc_final: 0.8175 (m-80) REVERT: H 110 LYS cc_start: 0.8419 (mmmt) cc_final: 0.7831 (mmtm) outliers start: 25 outliers final: 17 residues processed: 315 average time/residue: 0.8627 time to fit residues: 309.8577 Evaluate side-chains 317 residues out of total 2914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 295 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 C residue 393 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 27 ASP Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 447 ARG Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 28 GLU Chi-restraints excluded: chain G residue 61 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 155 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 258 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 200 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 338 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 GLN ** C 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.081753 restraints weight = 112848.616| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.72 r_work: 0.2674 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- 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 = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29210 Z= 0.169 Angle : 0.592 8.161 39714 Z= 0.320 Chirality : 0.047 0.175 4022 Planarity : 0.005 0.040 5284 Dihedral : 4.817 23.867 4010 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.46 % Allowed : 11.10 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3550 helix: 1.84 (0.20), residues: 656 sheet: 0.36 (0.20), residues: 716 loop : -0.14 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 22 TYR 0.028 0.002 TYR A 661 PHE 0.015 0.002 PHE A 187 TRP 0.014 0.002 TRP C 473 HIS 0.006 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00390 (29210) covalent geometry : angle 0.59166 (39714) hydrogen bonds : bond 0.04683 ( 1020) hydrogen bonds : angle 5.01842 ( 3352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10641.33 seconds wall clock time: 181 minutes 54.44 seconds (10914.44 seconds total)