Starting phenix.real_space_refine on Sun Apr 5 22:04:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qh6_53156/04_2026/9qh6_53156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qh6_53156/04_2026/9qh6_53156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qh6_53156/04_2026/9qh6_53156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qh6_53156/04_2026/9qh6_53156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qh6_53156/04_2026/9qh6_53156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qh6_53156/04_2026/9qh6_53156.map" } resolution = 3.2 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= 0.001 sd= 0.023 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 3 5.21 5 S 51 5.16 5 C 8499 2.51 5 N 2471 2.21 5 O 2459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13496 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1897 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 240} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1933 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 14, 'TRANS': 242} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1917 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1929 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 240} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1894 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 242} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "F" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1812 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 13, 'TRANS': 239} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 1964 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 366 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 20, 'GLU:plan': 8, 'TRP:plan': 1, 'ASP:plan': 11, 'TYR:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 210 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.21 Number of scatterers: 13496 At special positions: 0 Unit cell: (101.52, 115.902, 124.362, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 13 15.00 Mg 3 11.99 O 2459 8.00 N 2471 7.00 C 8499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 68 " distance=2.03 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: 0.76 Conformation dependent library (CDL) restraints added in 637.3 milliseconds 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3334 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 20 sheets defined 51.0% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.607A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 120 removed outlier: 4.210A pdb=" N THR A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 114 through 120' Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.507A pdb=" N VAL A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.888A pdb=" N GLY A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 removed outlier: 3.501A pdb=" N VAL A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.534A pdb=" N GLU A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.602A pdb=" N ILE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'B' and resid 47 through 60 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.749A pdb=" N LEU B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 102 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.610A pdb=" N VAL B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.992A pdb=" N GLU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 211 removed outlier: 4.061A pdb=" N GLY B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.534A pdb=" N VAL B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.736A pdb=" N LEU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.597A pdb=" N LEU C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 117 through 126 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 193 removed outlier: 4.173A pdb=" N GLU C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 212 removed outlier: 3.660A pdb=" N GLY C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.700A pdb=" N VAL C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 254 through 270 Processing helix chain 'D' and resid 23 through 34 removed outlier: 3.595A pdb=" N ASN D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 93 through 102 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 180 through 193 removed outlier: 3.854A pdb=" N GLU D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 removed outlier: 4.200A pdb=" N GLY D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 236 removed outlier: 3.702A pdb=" N VAL D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.706A pdb=" N ILE D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.582A pdb=" N GLY D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 34 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.683A pdb=" N LEU E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 114 through 116 No H-bonds generated for 'chain 'E' and resid 114 through 116' Processing helix chain 'E' and resid 117 through 125 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 180 through 193 removed outlier: 4.014A pdb=" N GLU E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 212 Processing helix chain 'E' and resid 222 through 236 removed outlier: 3.662A pdb=" N VAL E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 248 removed outlier: 3.512A pdb=" N ILE E 248 " --> pdb=" O GLU E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'F' and resid 23 through 35 removed outlier: 3.816A pdb=" N ASN F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.552A pdb=" N ILE F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 102 Processing helix chain 'F' and resid 114 through 116 No H-bonds generated for 'chain 'F' and resid 114 through 116' Processing helix chain 'F' and resid 117 through 126 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 180 through 193 removed outlier: 3.927A pdb=" N GLU F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 212 Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.505A pdb=" N VAL F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'G' and resid 383 through 400 removed outlier: 3.653A pdb=" N ARG G 389 " --> pdb=" O ARG G 385 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 400 " --> pdb=" O GLN G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 431 removed outlier: 3.720A pdb=" N VAL G 422 " --> pdb=" O ALA G 418 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 469 through 489 Processing helix chain 'G' and resid 519 through 527 removed outlier: 3.628A pdb=" N ARG G 523 " --> pdb=" O ALA G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 550 removed outlier: 3.611A pdb=" N GLY G 539 " --> pdb=" O ARG G 535 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN G 550 " --> pdb=" O GLY G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 590 Processing helix chain 'G' and resid 606 through 611 Processing helix chain 'G' and resid 621 through 623 No H-bonds generated for 'chain 'G' and resid 621 through 623' Processing helix chain 'G' and resid 624 through 638 Proline residue: G 630 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 67 removed outlier: 6.591A pdb=" N TYR A 64 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASP A 108 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 66 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 39 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.556A pdb=" N TYR B 64 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP B 108 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 66 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 133 Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 67 removed outlier: 6.419A pdb=" N TYR C 64 " --> pdb=" O TYR C 106 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP C 108 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 66 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 39 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 84 Processing sheet with id=AA9, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB1, first strand: chain 'D' and resid 63 through 67 removed outlier: 6.034A pdb=" N CYS D 105 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N SER D 151 " --> pdb=" O CYS D 105 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU D 107 " --> pdb=" O SER D 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 83 Processing sheet with id=AB3, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AB4, first strand: chain 'E' and resid 63 through 67 removed outlier: 6.059A pdb=" N CYS E 105 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER E 151 " --> pdb=" O CYS E 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU E 107 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 79 through 83 Processing sheet with id=AB6, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AB7, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.009A pdb=" N CYS F 105 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N SER F 151 " --> pdb=" O CYS F 105 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU F 107 " --> pdb=" O SER F 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.788A pdb=" N LYS F 84 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU F 87 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 130 through 133 Processing sheet with id=AC1, first strand: chain 'G' and resid 348 through 351 removed outlier: 3.801A pdb=" N VAL G 366 " --> pdb=" O TYR G 351 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 509 " --> pdb=" O ASN G 371 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE G 494 " --> pdb=" O CYS G 510 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG G 491 " --> pdb=" O LEU G 449 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA G 450 " --> pdb=" O LEU G 556 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU G 558 " --> pdb=" O ALA G 450 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER G 452 " --> pdb=" O LEU G 558 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE G 560 " --> pdb=" O SER G 452 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU G 454 " --> pdb=" O ILE G 560 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ARG G 555 " --> pdb=" O ALA G 593 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N HIS G 595 " --> pdb=" O ARG G 555 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU G 557 " --> pdb=" O HIS G 595 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE G 597 " --> pdb=" O LEU G 557 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL G 559 " --> pdb=" O ILE G 597 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N SER G 617 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY G 596 " --> pdb=" O SER G 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 406 through 410 removed outlier: 5.808A pdb=" N TRP G 439 " --> pdb=" O GLY G 409 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU G 415 " --> pdb=" O ARG G 440 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1941 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: 2.09 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4631 1.34 - 1.46: 2785 1.46 - 1.58: 6217 1.58 - 1.70: 16 1.70 - 1.81: 82 Bond restraints: 13731 Sorted by residual: bond pdb=" C4 ADP D 301 " pdb=" C5 ADP D 301 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.25e+00 bond pdb=" C4 ADP E 301 " pdb=" C5 ADP E 301 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C2' ADP D 301 " pdb=" C3' ADP D 301 " ideal model delta sigma weight residual 1.524 1.509 0.015 2.00e-02 2.50e+03 5.50e-01 bond pdb=" CA ILE E 248 " pdb=" CB ILE E 248 " ideal model delta sigma weight residual 1.545 1.539 0.006 9.10e-03 1.21e+04 5.07e-01 bond pdb=" CA GLU G 353 " pdb=" C GLU G 353 " ideal model delta sigma weight residual 1.529 1.522 0.007 1.04e-02 9.25e+03 5.03e-01 ... (remaining 13726 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 18164 1.21 - 2.41: 415 2.41 - 3.62: 92 3.62 - 4.83: 26 4.83 - 6.04: 11 Bond angle restraints: 18708 Sorted by residual: angle pdb=" N VAL G 637 " pdb=" CA VAL G 637 " pdb=" C VAL G 637 " ideal model delta sigma weight residual 113.43 110.18 3.25 1.09e+00 8.42e-01 8.88e+00 angle pdb=" N ILE D 248 " pdb=" CA ILE D 248 " pdb=" C ILE D 248 " ideal model delta sigma weight residual 111.62 109.63 1.99 7.90e-01 1.60e+00 6.32e+00 angle pdb=" C MET B 247 " pdb=" N ILE B 248 " pdb=" CA ILE B 248 " ideal model delta sigma weight residual 123.16 120.52 2.64 1.06e+00 8.90e-01 6.22e+00 angle pdb=" N ILE F 248 " pdb=" CA ILE F 248 " pdb=" C ILE F 248 " ideal model delta sigma weight residual 111.67 109.40 2.27 9.50e-01 1.11e+00 5.69e+00 angle pdb=" C PRO G 374 " pdb=" N GLU G 375 " pdb=" CA GLU G 375 " ideal model delta sigma weight residual 120.90 124.15 -3.25 1.41e+00 5.03e-01 5.30e+00 ... (remaining 18703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 8114 24.11 - 48.21: 206 48.21 - 72.32: 18 72.32 - 96.42: 2 96.42 - 120.53: 2 Dihedral angle restraints: 8342 sinusoidal: 3154 harmonic: 5188 Sorted by residual: dihedral pdb=" C5' ADP E 301 " pdb=" O5' ADP E 301 " pdb=" PA ADP E 301 " pdb=" O2A ADP E 301 " ideal model delta sinusoidal sigma weight residual 300.00 179.47 120.53 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1B ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PB ADP E 301 " pdb=" PA ADP E 301 " ideal model delta sinusoidal sigma weight residual -60.00 57.04 -117.04 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" C5' ADP D 301 " pdb=" O5' ADP D 301 " pdb=" PA ADP D 301 " pdb=" O2A ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 -150.23 90.23 1 2.00e+01 2.50e-03 2.41e+01 ... (remaining 8339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1313 0.026 - 0.051: 558 0.051 - 0.077: 187 0.077 - 0.103: 65 0.103 - 0.128: 72 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA VAL C 172 " pdb=" N VAL C 172 " pdb=" C VAL C 172 " pdb=" CB VAL C 172 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA VAL E 172 " pdb=" N VAL E 172 " pdb=" C VAL E 172 " pdb=" CB VAL E 172 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE E 130 " pdb=" N ILE E 130 " pdb=" C ILE E 130 " pdb=" CB ILE E 130 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 2192 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 401 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO G 402 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO G 402 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 402 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 164 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO C 165 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 165 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 165 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 15 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO E 16 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 16 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 16 " 0.017 5.00e-02 4.00e+02 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 10 2.51 - 3.11: 9566 3.11 - 3.71: 18740 3.71 - 4.30: 26697 4.30 - 4.90: 46607 Nonbonded interactions: 101620 Sorted by model distance: nonbonded pdb=" O2B ATP A 301 " pdb="MG MG A 302 " model vdw 1.917 2.170 nonbonded pdb=" O2B ATP C 301 " pdb="MG MG C 302 " model vdw 1.919 2.170 nonbonded pdb=" O3G ATP C 301 " pdb="MG MG C 302 " model vdw 1.940 2.170 nonbonded pdb=" O3G ATP A 301 " pdb="MG MG A 302 " model vdw 1.976 2.170 nonbonded pdb=" OG1 THR B 49 " pdb="MG MG B 302 " model vdw 2.032 2.170 ... (remaining 101615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 23 or (resid 24 and (name N or name CA or name C or name \ O or name CB )) or resid 25 through 28 or (resid 29 through 33 and (name N or na \ me CA or name C or name O or name CB )) or resid 34 through 43 or (resid 44 and \ (name N or name CA or name C or name O or name CB )) or resid 45 through 69 or ( \ resid 70 through 72 and (name N or name CA or name C or name O or name CB )) or \ resid 73 through 86 or (resid 87 and (name N or name CA or name C or name O or n \ ame CB )) or resid 88 through 111 or (resid 112 through 113 and (name N or name \ CA or name C or name O or name CB )) or resid 114 through 124 or (resid 125 thro \ ugh 128 and (name N or name CA or name C or name O or name CB )) or resid 129 th \ rough 138 or (resid 139 and (name N or name CA or name C or name O or name CB )) \ or resid 140 or (resid 141 through 143 and (name N or name CA or name C or name \ O or name CB )) or resid 144 through 155 or (resid 156 through 163 and (name N \ or name CA or name C or name O or name CB )) or resid 164 through 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throug \ h 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) or \ resid 181 through 182 or (resid 183 and (name N or name CA or name C or name O o \ r name CB )) or resid 184 through 186 or (resid 187 and (name N or name CA or na \ me C or name O or name CB )) or resid 188 through 196 or (resid 197 and (name N \ or name CA or name C or name O or name CB )) or resid 198 through 211 or (resid \ 212 through 213 and (name N or name CA or name C or name O or name CB )) or (res \ id 214 through 218 and (name N or name CA or name C or name O or name CB )) or r \ esid 219 through 221 or (resid 222 and (name N or name CA or name C or name O or \ name CB )) or resid 223 through 233 or (resid 234 through 235 and (name N or na \ me CA or name C or name O or name CB )) or resid 236 through 253 or (resid 254 t \ hrough 256 and (name N or name CA or name C or name O or name CB )) or resid 257 \ through 258 or (resid 259 and (name N or name CA or name C or name O or name CB \ )) or resid 260 through 262 or (resid 263 and (name N or name CA or name C or n \ ame O or name CB )) or resid 264 through 269)) selection = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or resid 22 or (resid 23 through 24 and (name N or name CA or na \ me C or name O or name CB )) or resid 25 through 28 or (resid 29 through 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 or (resid 35 an \ d (name N or name CA or name C or name O or name CB )) or resid 36 through 43 or \ (resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 \ through 70 or (resid 71 through 72 and (name N or name CA or name C or name O or \ name CB )) or resid 73 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 86 or (resid 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 111 or (resid 112 thro \ ugh 113 and (name N or name CA or name C or name O or name CB )) or resid 114 or \ (resid 115 through 116 and (name N or name CA or name C or name O or name CB )) \ or resid 117 through 125 or (resid 126 through 128 and (name N or name CA or na \ me C or name O or name CB )) or resid 129 through 133 or (resid 134 and (name N \ or name CA or name C or name O or name CB )) or resid 135 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 155 or (resid 156 through 163 and (name N or name CA or name C or name O or na \ me CB )) or resid 164 through 176 or (resid 177 and (name N or name CA or name C \ or name O or name CB )) or resid 178 through 179 or (resid 180 and (name N or n \ ame CA or name C or name O or name CB )) or resid 181 through 182 or (resid 183 \ and (name N or name CA or name C or name O or name CB )) or resid 184 through 18 \ 5 or (resid 186 through 187 and (name N or name CA or name C or name O or name C \ B )) or resid 188 through 194 or (resid 195 through 197 and (name N or name CA o \ r name C or name O or name CB )) or resid 198 through 211 or (resid 212 through \ 213 and (name N or name CA or name C or name O or name CB )) or (resid 214 throu \ gh 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thr \ ough 221 or (resid 222 and (name N or name CA or name C or name O or name CB )) \ or resid 223 through 233 or (resid 234 through 235 and (name N or name CA or nam \ e C or name O or name CB )) or resid 236 through 255 or (resid 256 and (name N o \ r name CA or name C or name O or name CB )) or resid 257 through 258 or (resid 2 \ 59 and (name N or name CA or name C or name O or name CB )) or resid 260 through \ 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) or r \ esid 264 through 269)) selection = (chain 'C' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or (resid 22 through 24 and (name N or name CA or name C or name \ O or name CB )) or resid 25 through 28 or (resid 29 through 33 and (name N or n \ ame CA or name C or name O or name CB )) or resid 34 or (resid 35 and (name N or \ name CA or name C or name O or name CB )) or resid 36 through 43 or (resid 44 a \ nd (name N or name CA or name C or name O or name CB )) or resid 45 through 69 o \ r (resid 70 through 72 and (name N or name CA or name C or name O or name CB )) \ or resid 73 through 83 or (resid 84 and (name N or name CA or name C or name O o \ r name CB )) or resid 85 through 86 or (resid 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 111 or (resid 112 through 113 and \ (name N or name CA or name C or name O or name CB )) or resid 114 or (resid 115 \ through 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 127 or (resid 128 and (name N or name CA or name C or name O or name C \ B )) or resid 129 through 138 or (resid 139 and (name N or name CA or name C or \ name O or name CB )) or resid 140 or (resid 141 through 143 and (name N or name \ CA or name C or name O or name CB )) or resid 144 through 155 or (resid 156 thro \ ugh 163 and (name N or name CA or name C or name O or name CB )) or resid 164 th \ rough 176 or (resid 177 and (name N or name CA or name C or name O or name CB )) \ or resid 178 through 179 or (resid 180 and (name N or name CA or name C or name \ O or name CB )) or resid 181 through 182 or (resid 183 and (name N or name CA o \ r name C or name O or name CB )) or resid 184 through 186 or (resid 187 and (nam \ e N or name CA or name C or name O or name CB )) or resid 188 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 211 or (resid 212 through 213 and (name N or name CA or name C \ or name O or name CB )) or (resid 214 through 218 and (name N or name CA or nam \ e C or name O or name CB )) or resid 219 through 221 or (resid 222 and (name N o \ r name CA or name C or name O or name CB )) or resid 223 through 233 or (resid 2 \ 34 through 235 and (name N or name CA or name C or name O or name CB )) or resid \ 236 through 262 or (resid 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 through 269)) selection = (chain 'D' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or resid 22 or (resid 23 through 24 and (name N or name CA or na \ me C or name O or name CB )) or resid 25 through 28 or (resid 29 through 33 and \ (name N or name CA or name C or name O or name CB )) or resid 34 or (resid 35 an \ d (name N or name CA or name C or name O or name CB )) or resid 36 through 43 or \ (resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 \ through 69 or (resid 70 through 72 and (name N or name CA or name C or name O or \ name CB )) or resid 73 through 83 or (resid 84 and (name N or name CA or name C \ or name O or name CB )) or resid 85 through 86 or (resid 87 and (name N or name \ CA or name C or name O or name CB )) or resid 88 through 111 or (resid 112 thro \ ugh 113 and (name N or name CA or name C or name O or name CB )) or resid 114 or \ (resid 115 through 116 and (name N or name CA or name C or name O or name CB )) \ or resid 117 through 124 or (resid 125 through 128 and (name N or name CA or na \ me C or name O or name CB )) or resid 129 through 133 or (resid 134 and (name N \ or name CA or name C or name O or name CB )) or resid 135 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 or (re \ sid 141 through 143 and (name N or name CA or name C or name O or name CB )) or \ resid 144 through 156 or (resid 157 through 163 and (name N or name CA or name C \ or name O or name CB )) or resid 164 through 182 or (resid 183 and (name N or n \ ame CA or name C or name O or name CB )) or resid 184 through 185 or (resid 186 \ through 187 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 8 through 194 or (resid 195 through 197 and (name N or name CA or name C or name \ O or name CB )) or resid 198 through 211 or (resid 212 through 213 and (name N \ or name CA or name C or name O or name CB )) or resid 214 or (resid 215 through \ 218 and (name N or name CA or name C or name O or name CB )) or resid 219 throug \ h 221 or (resid 222 and (name N or name CA or name C or name O or name CB )) or \ resid 223 through 233 or (resid 234 through 235 and (name N or name CA or name C \ or name O or name CB )) or resid 236 through 239 or (resid 240 and (name N or n \ ame CA or name C or name O or name CB )) or resid 241 through 258 or (resid 259 \ and (name N or name CA or name C or name O or name CB )) or resid 260 through 26 \ 2 or (resid 263 and (name N or name CA or name C or name O or name CB )) or resi \ d 264 through 269)) selection = (chain 'E' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 through 20 or (resid 21 and (name N or name CA or name C or name \ O or name CB )) or (resid 22 through 24 and (name N or name CA or name C or name \ O or name CB )) or resid 25 through 28 or (resid 29 through 33 and (name N or n \ ame CA or name C or name O or name CB )) or resid 34 or (resid 35 and (name N or \ name CA or name C or name O or name CB )) or resid 36 through 43 or (resid 44 a \ nd (name N or name CA or name C or name O or name CB )) or resid 45 through 71 o \ r (resid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 \ through 83 or (resid 84 and (name N or name CA or name C or name O or name CB ) \ ) or resid 85 through 86 or (resid 87 and (name N or name CA or name C or name O \ or name CB )) or resid 88 through 111 or (resid 112 through 113 and (name N or \ name CA or name C or name O or name CB )) or resid 114 or (resid 115 through 116 \ and (name N or name CA or name C or name O or name CB )) or resid 117 through 1 \ 24 or (resid 125 through 128 and (name N or name CA or name C or name O or name \ CB )) or resid 129 through 133 or (resid 134 and (name N or name CA or name C or \ name O or name CB )) or resid 135 through 140 or (resid 141 through 143 and (na \ me N or name CA or name C or name O or name CB )) or resid 144 through 155 or (r \ esid 156 through 163 and (name N or name CA or name C or name O or name CB )) or \ resid 164 through 176 or (resid 177 and (name N or name CA or name C or name O \ or name CB )) or resid 178 through 182 or (resid 183 and (name N or name CA or n \ ame C or name O or name CB )) or resid 184 through 186 or (resid 187 and (name N \ or name CA or name C or name O or name CB )) or resid 188 through 194 or (resid \ 195 through 197 and (name N or name CA or name C or name O or name CB )) or res \ id 198 through 221 or (resid 222 and (name N or name CA or name C or name O or n \ ame CB )) or resid 223 through 233 or (resid 234 through 235 and (name N or name \ CA or name C or name O or name CB )) or resid 236 through 269)) selection = (chain 'F' and (resid 17 through 22 or (resid 23 through 24 and (name N or name \ CA or name C or name O or name CB )) or resid 25 through 34 or (resid 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 115 or (re \ sid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 th \ rough 124 or (resid 125 through 128 and (name N or name CA or name C or name O o \ r name CB )) or resid 129 through 138 or (resid 139 and (name N or name CA or na \ me C or name O or name CB )) or resid 140 or (resid 141 through 143 and (name N \ or name CA or name C or name O or name CB )) or resid 144 through 185 or (resid \ 186 through 187 and (name N or name CA or name C or name O or name CB )) or resi \ d 188 through 211 or (resid 212 through 213 and (name N or name CA or name C or \ name O or name CB )) or (resid 214 through 218 and (name N or name CA or name C \ or name O or name CB )) or resid 219 through 253 or (resid 254 through 256 and ( \ name N or name CA or name C or name O or name CB )) or resid 257 through 258 or \ (resid 259 and (name N or name CA or name C or name O or name CB )) or resid 260 \ through 262 or (resid 263 and (name N or name CA or name C or name O or name CB \ )) or resid 264 through 269)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13732 Z= 0.130 Angle : 0.511 6.035 18710 Z= 0.274 Chirality : 0.038 0.128 2195 Planarity : 0.004 0.038 2429 Dihedral : 10.466 120.530 5005 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.43 % Allowed : 3.51 % Favored : 95.06 % 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: 0.28 (0.19), residues: 1803 helix: 0.61 (0.17), residues: 827 sheet: 1.25 (0.28), residues: 332 loop : -0.86 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 183 TYR 0.010 0.001 TYR D 152 PHE 0.008 0.001 PHE D 171 TRP 0.004 0.001 TRP G 483 HIS 0.002 0.000 HIS G 570 Details of bonding type rmsd covalent geometry : bond 0.00295 (13731) covalent geometry : angle 0.51091 (18708) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.29675 ( 2) hydrogen bonds : bond 0.27454 ( 680) hydrogen bonds : angle 7.31762 ( 1941) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 300 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8801 (t0) cc_final: 0.8584 (t0) REVERT: A 164 LYS cc_start: 0.9427 (mtpt) cc_final: 0.9119 (mtmm) REVERT: B 73 SER cc_start: 0.9135 (p) cc_final: 0.8749 (p) REVERT: C 73 SER cc_start: 0.9158 (p) cc_final: 0.8756 (p) REVERT: D 258 LYS cc_start: 0.9133 (mttt) cc_final: 0.8927 (mttp) REVERT: E 21 GLN cc_start: 0.9083 (pp30) cc_final: 0.8762 (pp30) REVERT: E 258 LYS cc_start: 0.9556 (mttt) cc_final: 0.9220 (mttm) REVERT: F 41 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8819 (mtmm) REVERT: F 140 ILE cc_start: 0.9352 (mt) cc_final: 0.8979 (mt) REVERT: F 208 LYS cc_start: 0.9284 (mmtm) cc_final: 0.9074 (mmmm) outliers start: 18 outliers final: 9 residues processed: 312 average time/residue: 0.1133 time to fit residues: 50.8937 Evaluate side-chains 212 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 599 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.0670 chunk 149 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 HIS D 122 HIS E 34 ASN G 433 GLN G 635 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.063648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.050089 restraints weight = 42788.583| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 4.06 r_work: 0.2510 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13732 Z= 0.103 Angle : 0.522 6.680 18710 Z= 0.264 Chirality : 0.038 0.162 2195 Planarity : 0.004 0.040 2429 Dihedral : 8.965 122.814 2148 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.67 % Allowed : 11.00 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.20), residues: 1803 helix: 1.73 (0.18), residues: 842 sheet: 1.36 (0.27), residues: 350 loop : -0.61 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.013 0.001 TYR F 152 PHE 0.012 0.001 PHE B 28 TRP 0.003 0.001 TRP G 483 HIS 0.002 0.000 HIS G 570 Details of bonding type rmsd covalent geometry : bond 0.00217 (13731) covalent geometry : angle 0.52227 (18708) SS BOND : bond 0.00352 ( 1) SS BOND : angle 0.60405 ( 2) hydrogen bonds : bond 0.03474 ( 680) hydrogen bonds : angle 4.79279 ( 1941) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ARG cc_start: 0.8256 (mmm160) cc_final: 0.6981 (ttm170) REVERT: A 151 SER cc_start: 0.9309 (t) cc_final: 0.9006 (p) REVERT: A 213 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8623 (tppp) REVERT: A 237 MET cc_start: 0.8650 (ttp) cc_final: 0.8406 (ttp) REVERT: B 158 ASN cc_start: 0.8493 (t0) cc_final: 0.8234 (t0) REVERT: B 237 MET cc_start: 0.8683 (ttp) cc_final: 0.8461 (ttt) REVERT: C 153 ASN cc_start: 0.8932 (m-40) cc_final: 0.8513 (m110) REVERT: E 21 GLN cc_start: 0.9603 (pp30) cc_final: 0.9332 (pp30) REVERT: E 112 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8765 (mm-30) REVERT: E 258 LYS cc_start: 0.9479 (mttt) cc_final: 0.9184 (mttm) REVERT: F 34 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8581 (t0) REVERT: F 108 ASP cc_start: 0.8587 (t0) cc_final: 0.8206 (t0) REVERT: G 417 ASP cc_start: 0.8592 (t0) cc_final: 0.8256 (t0) REVERT: G 435 SER cc_start: 0.9516 (m) cc_final: 0.9203 (t) REVERT: G 476 GLU cc_start: 0.9556 (mt-10) cc_final: 0.9190 (pt0) REVERT: G 506 PHE cc_start: 0.8722 (m-80) cc_final: 0.8474 (m-80) outliers start: 21 outliers final: 7 residues processed: 243 average time/residue: 0.1203 time to fit residues: 42.2294 Evaluate side-chains 220 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 55 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 151 optimal weight: 0.0370 chunk 176 optimal weight: 10.0000 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 550 GLN G 635 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.048692 restraints weight = 43978.598| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 4.21 r_work: 0.2477 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13732 Z= 0.111 Angle : 0.512 10.242 18710 Z= 0.252 Chirality : 0.038 0.130 2195 Planarity : 0.004 0.041 2429 Dihedral : 8.908 123.518 2143 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.51 % Allowed : 12.51 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.20), residues: 1803 helix: 2.27 (0.18), residues: 833 sheet: 1.30 (0.26), residues: 340 loop : -0.54 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 241 TYR 0.018 0.001 TYR F 152 PHE 0.016 0.001 PHE G 607 TRP 0.003 0.001 TRP G 483 HIS 0.002 0.000 HIS G 570 Details of bonding type rmsd covalent geometry : bond 0.00253 (13731) covalent geometry : angle 0.51220 (18708) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.46405 ( 2) hydrogen bonds : bond 0.03153 ( 680) hydrogen bonds : angle 4.37165 ( 1941) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 SER cc_start: 0.9300 (t) cc_final: 0.8956 (p) REVERT: A 213 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8486 (tppp) REVERT: B 71 ASP cc_start: 0.9391 (t0) cc_final: 0.9161 (t0) REVERT: B 158 ASN cc_start: 0.8482 (t0) cc_final: 0.8152 (t0) REVERT: B 237 MET cc_start: 0.8691 (ttp) cc_final: 0.8450 (ttt) REVERT: C 153 ASN cc_start: 0.8608 (m-40) cc_final: 0.8274 (m-40) REVERT: C 157 GLN cc_start: 0.8490 (pm20) cc_final: 0.8233 (mp10) REVERT: D 21 GLN cc_start: 0.9271 (pt0) cc_final: 0.8868 (pp30) REVERT: D 112 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8650 (mm-30) REVERT: D 213 LYS cc_start: 0.9068 (tptp) cc_final: 0.8689 (tppt) REVERT: E 21 GLN cc_start: 0.9609 (pp30) cc_final: 0.9275 (tm-30) REVERT: E 112 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8864 (mm-30) REVERT: F 108 ASP cc_start: 0.8644 (t0) cc_final: 0.8255 (t0) REVERT: F 109 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8499 (mm-40) REVERT: G 417 ASP cc_start: 0.8690 (t0) cc_final: 0.7946 (t0) REVERT: G 435 SER cc_start: 0.9502 (m) cc_final: 0.9220 (t) REVERT: G 476 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9145 (pt0) outliers start: 19 outliers final: 9 residues processed: 234 average time/residue: 0.1054 time to fit residues: 36.4213 Evaluate side-chains 216 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 ASN G 433 GLN G 635 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.048720 restraints weight = 43310.567| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 4.13 r_work: 0.2486 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13732 Z= 0.105 Angle : 0.500 8.517 18710 Z= 0.247 Chirality : 0.038 0.127 2195 Planarity : 0.003 0.039 2429 Dihedral : 8.799 122.681 2143 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.83 % Allowed : 12.27 % Favored : 85.90 % 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: 1.79 (0.20), residues: 1803 helix: 2.35 (0.18), residues: 840 sheet: 1.31 (0.26), residues: 350 loop : -0.56 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.019 0.001 TYR F 152 PHE 0.015 0.001 PHE G 611 TRP 0.003 0.000 TRP G 483 HIS 0.002 0.000 HIS G 570 Details of bonding type rmsd covalent geometry : bond 0.00240 (13731) covalent geometry : angle 0.49960 (18708) SS BOND : bond 0.00177 ( 1) SS BOND : angle 0.46313 ( 2) hydrogen bonds : bond 0.02819 ( 680) hydrogen bonds : angle 4.13557 ( 1941) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8519 (t0) cc_final: 0.8280 (t0) REVERT: A 114 ARG cc_start: 0.8267 (mmm160) cc_final: 0.6944 (ttm170) REVERT: A 151 SER cc_start: 0.9279 (t) cc_final: 0.8956 (p) REVERT: A 213 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8556 (tppp) REVERT: A 237 MET cc_start: 0.8838 (ttp) cc_final: 0.8578 (ttp) REVERT: A 249 GLU cc_start: 0.9265 (mm-30) cc_final: 0.9053 (mm-30) REVERT: B 71 ASP cc_start: 0.9423 (t0) cc_final: 0.9130 (t0) REVERT: B 158 ASN cc_start: 0.8586 (t0) cc_final: 0.8195 (t0) REVERT: B 237 MET cc_start: 0.8739 (ttp) cc_final: 0.8537 (ttt) REVERT: C 21 GLN cc_start: 0.9530 (OUTLIER) cc_final: 0.9245 (tm-30) REVERT: D 21 GLN cc_start: 0.9282 (pt0) cc_final: 0.8870 (pp30) REVERT: D 112 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8499 (mm-30) REVERT: E 21 GLN cc_start: 0.9589 (pp30) cc_final: 0.9253 (tm-30) REVERT: F 108 ASP cc_start: 0.8669 (t0) cc_final: 0.8311 (t0) REVERT: F 109 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8573 (mm-40) REVERT: F 164 LYS cc_start: 0.7804 (ptmm) cc_final: 0.7581 (pttp) REVERT: G 417 ASP cc_start: 0.8759 (t0) cc_final: 0.7934 (t0) REVERT: G 435 SER cc_start: 0.9467 (m) cc_final: 0.9196 (t) REVERT: G 476 GLU cc_start: 0.9542 (mt-10) cc_final: 0.9126 (pt0) REVERT: G 555 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8342 (mtt90) outliers start: 23 outliers final: 12 residues processed: 238 average time/residue: 0.1124 time to fit residues: 39.2190 Evaluate side-chains 224 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 488 CYS Chi-restraints excluded: chain G residue 555 ARG Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN G 635 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.058957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.045485 restraints weight = 44837.579| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 4.15 r_work: 0.2410 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13732 Z= 0.274 Angle : 0.614 7.549 18710 Z= 0.307 Chirality : 0.041 0.148 2195 Planarity : 0.004 0.038 2429 Dihedral : 9.221 124.324 2142 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.31 % Allowed : 11.87 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.20), residues: 1803 helix: 2.27 (0.18), residues: 849 sheet: 1.05 (0.25), residues: 352 loop : -0.57 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 183 TYR 0.018 0.001 TYR F 152 PHE 0.013 0.001 PHE G 611 TRP 0.004 0.001 TRP E 90 HIS 0.003 0.001 HIS G 592 Details of bonding type rmsd covalent geometry : bond 0.00630 (13731) covalent geometry : angle 0.61385 (18708) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.56579 ( 2) hydrogen bonds : bond 0.03982 ( 680) hydrogen bonds : angle 4.46756 ( 1941) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8946 (tt) REVERT: A 213 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8457 (tppp) REVERT: A 237 MET cc_start: 0.9016 (ttp) cc_final: 0.8740 (ttp) REVERT: B 71 ASP cc_start: 0.9492 (t0) cc_final: 0.9174 (t0) REVERT: B 158 ASN cc_start: 0.8874 (t0) cc_final: 0.8537 (t0) REVERT: B 237 MET cc_start: 0.8967 (ttp) cc_final: 0.8732 (ttt) REVERT: C 21 GLN cc_start: 0.9543 (OUTLIER) cc_final: 0.9248 (tm-30) REVERT: C 153 ASN cc_start: 0.9078 (m110) cc_final: 0.8759 (m-40) REVERT: C 161 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8183 (mtpt) REVERT: C 244 GLU cc_start: 0.9233 (tt0) cc_final: 0.8882 (pt0) REVERT: D 21 GLN cc_start: 0.9266 (pt0) cc_final: 0.8894 (pp30) REVERT: D 112 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8569 (mm-30) REVERT: E 21 GLN cc_start: 0.9567 (pp30) cc_final: 0.9267 (tm-30) REVERT: E 116 ASP cc_start: 0.9066 (t0) cc_final: 0.8580 (t0) REVERT: E 151 SER cc_start: 0.9358 (t) cc_final: 0.8818 (m) REVERT: F 108 ASP cc_start: 0.8851 (t0) cc_final: 0.8510 (t0) REVERT: F 109 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8676 (mm-40) REVERT: F 164 LYS cc_start: 0.7985 (ptmm) cc_final: 0.7725 (pttp) REVERT: G 417 ASP cc_start: 0.8928 (t0) cc_final: 0.8369 (t0) REVERT: G 476 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9107 (mp0) outliers start: 29 outliers final: 22 residues processed: 222 average time/residue: 0.1125 time to fit residues: 36.5098 Evaluate side-chains 225 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 488 CYS Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 555 ARG Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 610 ILE Chi-restraints excluded: chain G residue 637 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 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 34 ASN C 153 ASN G 635 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.047543 restraints weight = 43750.498| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 4.20 r_work: 0.2452 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13732 Z= 0.128 Angle : 0.527 9.348 18710 Z= 0.261 Chirality : 0.039 0.131 2195 Planarity : 0.003 0.039 2429 Dihedral : 9.046 122.423 2142 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.99 % Favored : 95.95 % Rotamer: Outliers : 2.15 % Allowed : 12.75 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.20), residues: 1803 helix: 2.44 (0.18), residues: 839 sheet: 1.12 (0.25), residues: 347 loop : -0.57 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 135 TYR 0.010 0.001 TYR A 152 PHE 0.011 0.001 PHE G 611 TRP 0.003 0.001 TRP G 483 HIS 0.001 0.000 HIS G 570 Details of bonding type rmsd covalent geometry : bond 0.00295 (13731) covalent geometry : angle 0.52718 (18708) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.61423 ( 2) hydrogen bonds : bond 0.02889 ( 680) hydrogen bonds : angle 4.11718 ( 1941) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8941 (tt) REVERT: A 213 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8494 (tppp) REVERT: A 237 MET cc_start: 0.8976 (ttp) cc_final: 0.8479 (ttt) REVERT: B 71 ASP cc_start: 0.9486 (t0) cc_final: 0.9156 (t0) REVERT: B 158 ASN cc_start: 0.8894 (t0) cc_final: 0.8579 (t0) REVERT: B 237 MET cc_start: 0.8878 (ttp) cc_final: 0.8668 (ttt) REVERT: C 21 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.9235 (tm-30) REVERT: C 161 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8177 (mtpt) REVERT: D 21 GLN cc_start: 0.9244 (pt0) cc_final: 0.8880 (pp30) REVERT: D 112 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8401 (mm-30) REVERT: E 21 GLN cc_start: 0.9558 (pp30) cc_final: 0.9268 (tm-30) REVERT: E 116 ASP cc_start: 0.9053 (t0) cc_final: 0.8525 (t0) REVERT: E 151 SER cc_start: 0.9346 (t) cc_final: 0.8830 (m) REVERT: F 108 ASP cc_start: 0.8719 (t0) cc_final: 0.8394 (t0) REVERT: F 109 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8677 (mm-40) REVERT: F 164 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7663 (pttp) REVERT: G 417 ASP cc_start: 0.8770 (t0) cc_final: 0.8203 (t0) REVERT: G 476 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9082 (pt0) REVERT: G 555 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8342 (mtt90) outliers start: 27 outliers final: 15 residues processed: 239 average time/residue: 0.1153 time to fit residues: 40.1244 Evaluate side-chains 232 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 488 CYS Chi-restraints excluded: chain G residue 555 ARG Chi-restraints excluded: chain G residue 607 PHE Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 8.9990 chunk 120 optimal weight: 0.0030 chunk 122 optimal weight: 7.9990 chunk 64 optimal weight: 0.0570 chunk 20 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.9310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN G 433 GLN G 570 HIS G 635 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.061876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.048384 restraints weight = 43380.328| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 4.13 r_work: 0.2488 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 13732 Z= 0.095 Angle : 0.517 7.343 18710 Z= 0.257 Chirality : 0.038 0.134 2195 Planarity : 0.003 0.048 2429 Dihedral : 8.788 119.479 2141 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 1.67 % Allowed : 14.10 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1803 helix: 2.53 (0.18), residues: 839 sheet: 1.25 (0.26), residues: 326 loop : -0.52 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 114 TYR 0.022 0.001 TYR F 106 PHE 0.011 0.001 PHE G 611 TRP 0.003 0.000 TRP F 90 HIS 0.001 0.000 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00216 (13731) covalent geometry : angle 0.51739 (18708) SS BOND : bond 0.00199 ( 1) SS BOND : angle 0.43540 ( 2) hydrogen bonds : bond 0.02549 ( 680) hydrogen bonds : angle 3.97107 ( 1941) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8954 (tt) REVERT: A 92 ASP cc_start: 0.8977 (m-30) cc_final: 0.8752 (m-30) REVERT: A 108 ASP cc_start: 0.8455 (t0) cc_final: 0.8239 (t0) REVERT: A 151 SER cc_start: 0.9235 (t) cc_final: 0.8942 (p) REVERT: A 213 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8505 (tppp) REVERT: A 237 MET cc_start: 0.8928 (ttp) cc_final: 0.8407 (ttt) REVERT: B 71 ASP cc_start: 0.9480 (t0) cc_final: 0.9157 (t0) REVERT: B 158 ASN cc_start: 0.8882 (t0) cc_final: 0.8581 (t0) REVERT: C 21 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9251 (tm-30) REVERT: C 161 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8232 (mtpt) REVERT: D 21 GLN cc_start: 0.9272 (pt0) cc_final: 0.8904 (pp30) REVERT: D 112 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8334 (mm-30) REVERT: E 21 GLN cc_start: 0.9546 (pp30) cc_final: 0.9239 (tm-30) REVERT: E 116 ASP cc_start: 0.8977 (t0) cc_final: 0.8442 (t0) REVERT: E 253 ASP cc_start: 0.9040 (m-30) cc_final: 0.8814 (m-30) REVERT: F 108 ASP cc_start: 0.8571 (t0) cc_final: 0.8241 (t0) REVERT: F 109 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8631 (mm-40) REVERT: F 164 LYS cc_start: 0.7827 (ptmm) cc_final: 0.7537 (pttp) REVERT: G 417 ASP cc_start: 0.8710 (t0) cc_final: 0.7879 (t0) REVERT: G 441 GLN cc_start: 0.8476 (mt0) cc_final: 0.8186 (mt0) REVERT: G 476 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9112 (pt0) REVERT: G 555 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8294 (mtt90) outliers start: 21 outliers final: 13 residues processed: 245 average time/residue: 0.1054 time to fit residues: 38.0483 Evaluate side-chains 233 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 488 CYS Chi-restraints excluded: chain G residue 555 ARG Chi-restraints excluded: chain G residue 607 PHE Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 153 ASN C 153 ASN G 433 GLN G 635 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.047472 restraints weight = 43695.917| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 4.16 r_work: 0.2466 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13732 Z= 0.131 Angle : 0.540 7.817 18710 Z= 0.270 Chirality : 0.039 0.170 2195 Planarity : 0.003 0.039 2429 Dihedral : 8.790 116.415 2141 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 1.75 % Allowed : 14.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1803 helix: 2.57 (0.19), residues: 836 sheet: 1.20 (0.26), residues: 336 loop : -0.49 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 97 TYR 0.009 0.001 TYR A 152 PHE 0.008 0.001 PHE B 28 TRP 0.003 0.000 TRP E 90 HIS 0.002 0.000 HIS G 575 Details of bonding type rmsd covalent geometry : bond 0.00305 (13731) covalent geometry : angle 0.53961 (18708) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.49179 ( 2) hydrogen bonds : bond 0.02816 ( 680) hydrogen bonds : angle 4.01644 ( 1941) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9001 (tt) REVERT: A 213 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8518 (tppp) REVERT: A 237 MET cc_start: 0.8987 (ttp) cc_final: 0.8432 (ttt) REVERT: B 71 ASP cc_start: 0.9495 (t0) cc_final: 0.9162 (t0) REVERT: B 158 ASN cc_start: 0.8971 (t0) cc_final: 0.8676 (t0) REVERT: C 21 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9246 (tm-30) REVERT: D 21 GLN cc_start: 0.9289 (pt0) cc_final: 0.8898 (pp30) REVERT: D 112 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8374 (mm-30) REVERT: E 21 GLN cc_start: 0.9535 (pp30) cc_final: 0.9229 (tm-30) REVERT: E 116 ASP cc_start: 0.9020 (t0) cc_final: 0.8493 (t0) REVERT: F 108 ASP cc_start: 0.8643 (t0) cc_final: 0.8329 (t0) REVERT: F 109 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8684 (mm-40) REVERT: F 164 LYS cc_start: 0.7915 (ptmm) cc_final: 0.7603 (pttp) REVERT: G 417 ASP cc_start: 0.8761 (t0) cc_final: 0.8171 (t0) REVERT: G 441 GLN cc_start: 0.8467 (mt0) cc_final: 0.8133 (mt0) REVERT: G 476 GLU cc_start: 0.9522 (mt-10) cc_final: 0.9114 (pt0) outliers start: 22 outliers final: 17 residues processed: 233 average time/residue: 0.1114 time to fit residues: 38.1084 Evaluate side-chains 235 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 488 CYS Chi-restraints excluded: chain G residue 607 PHE Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.8980 chunk 155 optimal weight: 0.0070 chunk 92 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 153 ASN G 635 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.062864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.049266 restraints weight = 43475.024| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 4.21 r_work: 0.2500 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13732 Z= 0.092 Angle : 0.530 8.303 18710 Z= 0.263 Chirality : 0.038 0.139 2195 Planarity : 0.003 0.039 2429 Dihedral : 8.647 110.053 2141 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.67 % Rotamer: Outliers : 1.43 % Allowed : 15.14 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.20), residues: 1803 helix: 2.50 (0.18), residues: 836 sheet: 1.22 (0.26), residues: 336 loop : -0.47 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 97 TYR 0.022 0.001 TYR F 106 PHE 0.009 0.001 PHE G 611 TRP 0.004 0.001 TRP E 90 HIS 0.001 0.000 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00209 (13731) covalent geometry : angle 0.53028 (18708) SS BOND : bond 0.00230 ( 1) SS BOND : angle 0.47442 ( 2) hydrogen bonds : bond 0.02348 ( 680) hydrogen bonds : angle 3.89135 ( 1941) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8988 (tt) REVERT: A 41 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8889 (mtpt) REVERT: A 109 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8755 (mm-40) REVERT: A 151 SER cc_start: 0.9286 (t) cc_final: 0.9023 (p) REVERT: A 152 TYR cc_start: 0.8970 (p90) cc_final: 0.8710 (p90) REVERT: A 213 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8543 (tppp) REVERT: A 237 MET cc_start: 0.8945 (ttp) cc_final: 0.8442 (ttt) REVERT: B 71 ASP cc_start: 0.9464 (t0) cc_final: 0.9136 (t0) REVERT: B 158 ASN cc_start: 0.8935 (t0) cc_final: 0.8660 (t0) REVERT: C 21 GLN cc_start: 0.9554 (OUTLIER) cc_final: 0.9264 (tm-30) REVERT: C 108 ASP cc_start: 0.8862 (t0) cc_final: 0.8527 (m-30) REVERT: C 157 GLN cc_start: 0.8806 (mp10) cc_final: 0.8539 (mp10) REVERT: D 21 GLN cc_start: 0.9289 (pt0) cc_final: 0.8903 (pp30) REVERT: D 87 GLU cc_start: 0.8769 (tt0) cc_final: 0.8404 (mm-30) REVERT: D 112 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8389 (mm-30) REVERT: E 21 GLN cc_start: 0.9532 (pp30) cc_final: 0.9232 (tm-30) REVERT: E 116 ASP cc_start: 0.8948 (t0) cc_final: 0.8409 (t0) REVERT: E 151 SER cc_start: 0.9381 (t) cc_final: 0.8813 (m) REVERT: E 152 TYR cc_start: 0.8818 (t80) cc_final: 0.8410 (t80) REVERT: F 164 LYS cc_start: 0.7839 (ptmm) cc_final: 0.7532 (pttp) REVERT: G 410 HIS cc_start: 0.8785 (m-70) cc_final: 0.8409 (m-70) REVERT: G 417 ASP cc_start: 0.8665 (t0) cc_final: 0.7820 (t0) REVERT: G 441 GLN cc_start: 0.8474 (mt0) cc_final: 0.8213 (mt0) REVERT: G 476 GLU cc_start: 0.9522 (mt-10) cc_final: 0.9123 (pt0) REVERT: G 517 MET cc_start: 0.7236 (ppp) cc_final: 0.6827 (ttp) outliers start: 18 outliers final: 11 residues processed: 241 average time/residue: 0.1052 time to fit residues: 37.6879 Evaluate side-chains 229 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 607 PHE Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN G 635 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.048656 restraints weight = 43520.599| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 4.18 r_work: 0.2492 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13732 Z= 0.115 Angle : 0.556 9.691 18710 Z= 0.275 Chirality : 0.039 0.146 2195 Planarity : 0.003 0.039 2429 Dihedral : 8.603 102.052 2141 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 1.27 % Allowed : 15.86 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1803 helix: 2.55 (0.19), residues: 836 sheet: 1.19 (0.26), residues: 346 loop : -0.50 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 97 TYR 0.011 0.001 TYR C 152 PHE 0.008 0.001 PHE G 611 TRP 0.003 0.000 TRP E 90 HIS 0.001 0.000 HIS F 69 Details of bonding type rmsd covalent geometry : bond 0.00270 (13731) covalent geometry : angle 0.55632 (18708) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.60970 ( 2) hydrogen bonds : bond 0.02653 ( 680) hydrogen bonds : angle 3.91495 ( 1941) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3606 Ramachandran restraints generated. 1803 Oldfield, 0 Emsley, 1803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8914 (tt) REVERT: A 41 LYS cc_start: 0.9168 (mtmt) cc_final: 0.8727 (mtpt) REVERT: A 151 SER cc_start: 0.9271 (t) cc_final: 0.9008 (p) REVERT: A 152 TYR cc_start: 0.9002 (p90) cc_final: 0.8784 (p90) REVERT: A 177 ASP cc_start: 0.9202 (t0) cc_final: 0.8947 (t0) REVERT: A 213 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8545 (tppp) REVERT: A 237 MET cc_start: 0.8997 (ttp) cc_final: 0.8456 (ttt) REVERT: B 71 ASP cc_start: 0.9464 (t0) cc_final: 0.9127 (t0) REVERT: B 158 ASN cc_start: 0.8991 (t0) cc_final: 0.8720 (t0) REVERT: C 21 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9263 (tm-30) REVERT: C 157 GLN cc_start: 0.8792 (mp10) cc_final: 0.8558 (mp10) REVERT: D 21 GLN cc_start: 0.9303 (pt0) cc_final: 0.8888 (pp30) REVERT: D 112 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8399 (mm-30) REVERT: E 21 GLN cc_start: 0.9536 (pp30) cc_final: 0.9227 (tm-30) REVERT: E 116 ASP cc_start: 0.8981 (t0) cc_final: 0.8442 (t0) REVERT: E 151 SER cc_start: 0.9363 (t) cc_final: 0.8816 (m) REVERT: E 152 TYR cc_start: 0.8836 (t80) cc_final: 0.8438 (t80) REVERT: F 108 ASP cc_start: 0.8569 (t0) cc_final: 0.8293 (t0) REVERT: F 164 LYS cc_start: 0.7891 (ptmm) cc_final: 0.7578 (pttp) REVERT: G 417 ASP cc_start: 0.8746 (t0) cc_final: 0.8154 (t0) REVERT: G 441 GLN cc_start: 0.8451 (mt0) cc_final: 0.8108 (mt0) REVERT: G 476 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9103 (pt0) REVERT: G 517 MET cc_start: 0.7306 (ppp) cc_final: 0.6593 (ttp) outliers start: 16 outliers final: 12 residues processed: 226 average time/residue: 0.0998 time to fit residues: 33.9953 Evaluate side-chains 230 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain D residue 152 TYR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 607 PHE Chi-restraints excluded: chain G residue 610 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 94 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 635 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.050311 restraints weight = 42818.898| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 4.22 r_work: 0.2517 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13732 Z= 0.091 Angle : 0.534 8.648 18710 Z= 0.264 Chirality : 0.038 0.139 2195 Planarity : 0.003 0.039 2429 Dihedral : 8.437 93.012 2141 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.20 % Allowed : 15.86 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1803 helix: 2.57 (0.19), residues: 822 sheet: 1.25 (0.26), residues: 346 loop : -0.47 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 97 TYR 0.025 0.001 TYR F 106 PHE 0.009 0.001 PHE G 611 TRP 0.004 0.000 TRP E 90 HIS 0.001 0.000 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00204 (13731) covalent geometry : angle 0.53365 (18708) SS BOND : bond 0.00276 ( 1) SS BOND : angle 0.55013 ( 2) hydrogen bonds : bond 0.02255 ( 680) hydrogen bonds : angle 3.82137 ( 1941) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.09 seconds wall clock time: 48 minutes 46.87 seconds (2926.87 seconds total)