Starting phenix.real_space_refine on Sun Apr 5 15:05:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhg_53163/04_2026/9qhg_53163.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhg_53163/04_2026/9qhg_53163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qhg_53163/04_2026/9qhg_53163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhg_53163/04_2026/9qhg_53163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qhg_53163/04_2026/9qhg_53163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhg_53163/04_2026/9qhg_53163.map" } resolution = 3.9 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 21 5.16 5 C 7022 2.51 5 N 2080 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 11094 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1532 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 14, 'TRANS': 239} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 575 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 6, 'ASP:plan': 18, 'GLU:plan': 17, 'ARG:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 249 Chain: "B" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1642 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 15, 'TRANS': 239} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 17, 'GLU:plan': 15, 'ARG:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 207 Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1715 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 15, 'TRANS': 240} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 16, 'ASN:plan1': 2, 'ARG:plan': 7, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 183 Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1672 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 15, 'TRANS': 239} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 18, 'ASN:plan1': 3, 'ARG:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 196 Chain: "E" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1588 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 15, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 364 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 17, 'GLN:plan1': 6, 'ARG:plan': 8, 'PHE:plan': 2, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 208 Chain: "F" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1376 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 13, 'TRANS': 229} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 522 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 18, 'ASN:plan1': 4, 'ARG:plan': 16, 'GLN:plan1': 5, 'TYR:plan': 3, 'PHE:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 279 Chain: "G" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1422 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLU:plan': 14, 'GLN:plan1': 5, 'ASP:plan': 18, 'ARG:plan': 18, 'PHE:plan': 3, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 255 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 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: 2.93, per 1000 atoms: 0.26 Number of scatterers: 11094 At special positions: 0 Unit cell: (120.978, 117.594, 96.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 13 15.00 O 1958 8.00 N 2080 7.00 C 7022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 636.7 milliseconds 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 19 sheets defined 53.7% alpha, 11.3% 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 21 through 32 Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 114 through 123 removed outlier: 4.430A pdb=" N VAL A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N HIS A 120 " --> pdb=" O THR A 116 " (cutoff:3.500A) Proline residue: A 121 - end of helix No H-bonds generated for 'chain 'A' and resid 114 through 123' Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.771A pdb=" N THR A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 220 through 234 Processing helix chain 'A' and resid 236 through 239 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.702A pdb=" N ASP A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.838A pdb=" N LEU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 76' Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'B' and resid 108 through 111 removed outlier: 3.663A pdb=" N ALA B 111 " --> pdb=" O VAL B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 111' Processing helix chain 'B' and resid 112 through 124 removed outlier: 4.611A pdb=" N VAL B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 193 through 211 removed outlier: 3.545A pdb=" N CYS B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Proline residue: B 199 - end of helix removed outlier: 3.571A pdb=" N ARG B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 234 removed outlier: 3.518A pdb=" N VAL B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.594A pdb=" N LEU B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.686A pdb=" N VAL C 25 " --> pdb=" O ASP C 21 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.765A pdb=" N THR C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.848A pdb=" N GLN C 167 " --> pdb=" O PRO C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 197 through 209 removed outlier: 3.650A pdb=" N ILE C 201 " --> pdb=" O CYS C 197 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.786A pdb=" N VAL C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.740A pdb=" N LEU C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR C 250 " --> pdb=" O ILE C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 250' Processing helix chain 'C' and resid 253 through 267 Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.686A pdb=" N VAL D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 108 through 111 Processing helix chain 'D' and resid 114 through 123 Proline residue: D 121 - end of helix Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 178 through 190 Processing helix chain 'D' and resid 193 through 210 Proline residue: D 199 - end of helix removed outlier: 3.633A pdb=" N ARG D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 234 removed outlier: 3.701A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.508A pdb=" N MET D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 253 through 267 removed outlier: 3.708A pdb=" N ARG D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 71 through 77 removed outlier: 4.006A pdb=" N LEU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 115 through 120 removed outlier: 3.659A pdb=" N LEU E 119 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 115 through 120' Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 158 through 161 removed outlier: 4.234A pdb=" N LEU E 161 " --> pdb=" O LEU E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 162 through 167 Processing helix chain 'E' and resid 178 through 190 Processing helix chain 'E' and resid 196 through 211 removed outlier: 3.653A pdb=" N LEU E 200 " --> pdb=" O ARG E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.804A pdb=" N VAL E 224 " --> pdb=" O SER E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 245 Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.744A pdb=" N THR E 250 " --> pdb=" O ILE E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 267 Processing helix chain 'F' and resid 22 through 32 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 72 through 76 removed outlier: 3.671A pdb=" N LEU F 75 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 99 removed outlier: 3.577A pdb=" N ALA F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 115 through 123 Proline residue: F 121 - end of helix Processing helix chain 'F' and resid 151 through 155 removed outlier: 3.621A pdb=" N GLN F 155 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'F' and resid 178 through 190 Processing helix chain 'F' and resid 193 through 209 Proline residue: F 199 - end of helix Processing helix chain 'F' and resid 221 through 234 Processing helix chain 'F' and resid 236 through 245 Processing helix chain 'F' and resid 245 through 250 removed outlier: 4.236A pdb=" N THR F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 267 removed outlier: 3.884A pdb=" N ARG F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY F 258 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 389 removed outlier: 3.757A pdb=" N ALA G 388 " --> pdb=" O GLU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 407 removed outlier: 3.539A pdb=" N ALA G 406 " --> pdb=" O ARG G 402 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU G 407 " --> pdb=" O GLN G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 438 Processing helix chain 'G' and resid 477 through 496 Processing helix chain 'G' and resid 525 through 534 removed outlier: 3.702A pdb=" N GLY G 534 " --> pdb=" O ARG G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 556 removed outlier: 4.392A pdb=" N ALA G 546 " --> pdb=" O ARG G 542 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN G 556 " --> pdb=" O ALA G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 597 Processing helix chain 'G' and resid 610 through 619 Processing helix chain 'G' and resid 635 through 645 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65 removed outlier: 5.976A pdb=" N TYR A 62 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 106 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 64 " --> pdb=" O ASP A 106 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS A 103 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N SER A 149 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A 105 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 64 removed outlier: 5.968A pdb=" N TYR B 62 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP B 106 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 64 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N CYS B 103 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER B 149 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 105 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 36 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR B 150 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU B 38 " --> pdb=" O TYR B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 82 Processing sheet with id=AA6, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.608A pdb=" N GLU B 136 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 64 removed outlier: 6.298A pdb=" N CYS C 103 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N SER C 149 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 105 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 36 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TYR C 150 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU C 38 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU C 37 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 81 Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.414A pdb=" N GLU C 136 " --> pdb=" O ILE C 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 61 through 65 removed outlier: 3.561A pdb=" N ASP D 106 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N CYS D 103 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER D 149 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU D 105 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 36 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N TYR D 150 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU D 38 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 77 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 131 Processing sheet with id=AB4, first strand: chain 'E' and resid 61 through 65 removed outlier: 3.511A pdb=" N TYR E 104 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 64 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS E 103 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER E 149 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU E 105 " --> pdb=" O SER E 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA E 148 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AB6, first strand: chain 'E' and resid 128 through 131 Processing sheet with id=AB7, first strand: chain 'F' and resid 61 through 64 removed outlier: 6.306A pdb=" N TYR F 62 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL F 36 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 150 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU F 38 " --> pdb=" O TYR F 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 80 Processing sheet with id=AB9, first strand: chain 'F' and resid 128 through 131 Processing sheet with id=AC1, first strand: chain 'G' and resid 514 through 518 removed outlier: 6.439A pdb=" N ILE G 501 " --> pdb=" O CYS G 517 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP G 498 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA G 457 " --> pdb=" O LEU G 563 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU G 565 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER G 459 " --> pdb=" O LEU G 565 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE G 567 " --> pdb=" O SER G 459 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU G 461 " --> pdb=" O ILE G 567 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER G 600 " --> pdb=" O ARG G 562 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1725 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: 1.98 Time building geometry restraints manager: 1.39 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: 3851 1.34 - 1.46: 2371 1.46 - 1.58: 5014 1.58 - 1.69: 20 1.69 - 1.81: 30 Bond restraints: 11286 Sorted by residual: bond pdb=" C4 ADP D 301 " pdb=" C5 ADP D 301 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.36e+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=" C ARG G 536 " pdb=" O ARG G 536 " ideal model delta sigma weight residual 1.248 1.237 0.012 1.26e-02 6.30e+03 8.59e-01 bond pdb=" N ALA C 111 " pdb=" CA ALA C 111 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" CA PRO B 152 " pdb=" C PRO B 152 " ideal model delta sigma weight residual 1.526 1.517 0.009 1.13e-02 7.83e+03 5.97e-01 ... (remaining 11281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 15026 1.17 - 2.34: 382 2.34 - 3.51: 118 3.51 - 4.68: 24 4.68 - 5.85: 19 Bond angle restraints: 15569 Sorted by residual: angle pdb=" CA GLU D 247 " pdb=" C GLU D 247 " pdb=" N PRO D 248 " ideal model delta sigma weight residual 120.81 118.40 2.41 8.60e-01 1.35e+00 7.83e+00 angle pdb=" C GLY F 212 " pdb=" N GLN F 213 " pdb=" CA GLN F 213 " ideal model delta sigma weight residual 121.54 126.41 -4.87 1.91e+00 2.74e-01 6.50e+00 angle pdb=" N VAL C 109 " pdb=" CA VAL C 109 " pdb=" C VAL C 109 " ideal model delta sigma weight residual 112.98 109.85 3.13 1.25e+00 6.40e-01 6.28e+00 angle pdb=" N PRO E 163 " pdb=" CA PRO E 163 " pdb=" C PRO E 163 " ideal model delta sigma weight residual 112.47 117.34 -4.87 2.06e+00 2.36e-01 5.58e+00 angle pdb=" C LEU E 158 " pdb=" N LYS E 159 " pdb=" CA LYS E 159 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.68e+00 ... (remaining 15564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 6320 17.04 - 34.07: 236 34.07 - 51.11: 61 51.11 - 68.14: 6 68.14 - 85.18: 5 Dihedral angle restraints: 6628 sinusoidal: 1609 harmonic: 5019 Sorted by residual: dihedral pdb=" CA THR D 134 " pdb=" C THR D 134 " pdb=" N GLY D 135 " pdb=" CA GLY D 135 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS E 162 " pdb=" C LYS E 162 " pdb=" N PRO E 163 " pdb=" CA PRO E 163 " ideal model delta harmonic sigma weight residual -180.00 -163.45 -16.55 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA MET B 235 " pdb=" C MET B 235 " pdb=" N ASN B 236 " pdb=" CA ASN B 236 " ideal model delta harmonic sigma weight residual 180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1303 0.032 - 0.064: 455 0.064 - 0.095: 120 0.095 - 0.127: 62 0.127 - 0.159: 3 Chirality restraints: 1943 Sorted by residual: chirality pdb=" CA PRO E 163 " pdb=" N PRO E 163 " pdb=" C PRO E 163 " pdb=" CB PRO E 163 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA ILE F 170 " pdb=" N ILE F 170 " pdb=" C ILE F 170 " pdb=" CB ILE F 170 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE D 172 " pdb=" N ILE D 172 " pdb=" C ILE D 172 " pdb=" CB ILE D 172 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1940 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 17 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 18 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 18 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 18 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 151 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO E 152 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 34 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 35 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 35 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 35 " -0.018 5.00e-02 4.00e+02 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 4280 2.89 - 3.39: 11102 3.39 - 3.90: 16923 3.90 - 4.40: 17352 4.40 - 4.90: 28703 Nonbonded interactions: 78360 Sorted by model distance: nonbonded pdb=" O ILE D 131 " pdb=" CA GLY D 135 " model vdw 2.388 2.752 nonbonded pdb=" O2' ADP D 301 " pdb=" O3' ADP D 301 " model vdw 2.496 2.432 nonbonded pdb=" O2' ADP E 301 " pdb=" O3' ADP E 301 " model vdw 2.500 2.432 nonbonded pdb=" O2' ATP A 301 " pdb=" O3' ATP A 301 " model vdw 2.618 2.432 nonbonded pdb=" N VAL C 109 " pdb=" N GLU C 110 " model vdw 2.625 2.560 ... (remaining 78355 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 21 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 or (resid 41 thro \ ugh 42 and (name N or name CA or name C or name O or name CB )) or (resid 43 thr \ ough 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 54 or (resid 55 through 57 and (name N or name CA or name C or name O or na \ me CB )) or resid 58 or (resid 59 through 61 and (name N or name CA or name C or \ name O or name CB )) or resid 62 or (resid 63 through 66 and (name N or name CA \ or name C or name O or name CB )) or (resid 71 through 75 and (name N or name C \ A or name C or name O or name CB )) or resid 76 through 78 or (resid 79 through \ 82 and (name N or name CA or name C or name O or name CB )) or (resid 83 through \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 through \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or res \ id 93 or (resid 94 through 99 and (name N or name CA or name C or name O or name \ CB )) or (resid 100 through 103 and (name N or name CA or name C or name O or n \ ame CB )) or resid 104 through 106 or (resid 107 through 119 and (name N or name \ CA or name C or name O or name CB )) or resid 120 through 121 or (resid 122 thr \ ough 129 and (name N or name CA or name C or name O or name CB )) or resid 130 t \ hrough 137 or (resid 138 through 142 and (name N or name CA or name C or name O \ or name CB )) or resid 143 or (resid 144 through 152 and (name N or name CA or n \ ame C or name O or name CB )) or resid 153 or (resid 154 through 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 169 or (resid \ 170 through 171 and (name N or name CA or name C or name O or name CB )) or res \ id 172 through 175 or (resid 176 through 190 and (name N or name CA or name C or \ name O or name CB )) or (resid 191 through 211 and (name N or name CA or name C \ or name O or name CB )) or (resid 212 through 223 and (name N or name CA or nam \ e C or name O or name CB )) or resid 224 through 228 or (resid 229 through 233 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 234 through 25 \ 0 and (name N or name CA or name C or name O or name CB )) or (resid 255 through \ 257 and (name N or name CA or name C or name O or name CB )) or resid 258 throu \ gh 267)) selection = (chain 'B' and ((resid 21 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and (n \ ame N or name CA or name C or name O or name CB )) or resid 37 through 40 or (re \ sid 41 through 42 and (name N or name CA or name C or name O or name CB )) or (r \ esid 43 through 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 or (resid 50 through 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 54 or (resid 55 through 57 and (name N or name CA o \ r name C or name O or name CB )) or resid 58 or (resid 59 through 61 and (name N \ or name CA or name C or name O or name CB )) or resid 62 through 63 or (resid 6 \ 4 through 66 and (name N or name CA or name C or name O or name CB )) or (resid \ 71 through 75 and (name N or name CA or name C or name O or name CB )) or resid \ 76 through 78 or (resid 79 through 82 and (name N or name CA or name C or name O \ or name CB )) or (resid 83 through 87 and (name N or name CA or name C or name \ O or name CB )) or resid 88 through 89 or (resid 90 and (name N or name CA or na \ me C or name O or name CB )) or resid 91 or (resid 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 or (resid 94 through 99 and (name N o \ r name CA or name C or name O or name CB )) or (resid 100 through 103 and (name \ N or name CA or name C or name O or name CB )) or resid 104 or (resid 105 throug \ h 119 and (name N or name CA or name C or name O or name CB )) or resid 120 thro \ ugh 121 or (resid 122 through 129 and (name N or name CA or name C or name O or \ name CB )) or resid 130 through 132 or (resid 133 through 134 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 135 through 142 and (name N or \ name CA or name C or name O or name CB )) or (resid 143 through 152 and (name N \ or name CA or name C or name O or name CB )) or resid 153 through 161 or (resid \ 162 and (name N or name CA or name C or name O or name CB )) or resid 163 throug \ h 166 or (resid 167 through 168 and (name N or name CA or name C or name O or na \ me CB )) or resid 169 or (resid 170 through 171 and (name N or name CA or name C \ or name O or name CB )) or resid 172 or (resid 173 and (name N or name CA or na \ me C or name O or name CB )) or resid 174 through 175 or (resid 176 through 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 or (resid \ 192 through 211 and (name N or name CA or name C or name O or name CB )) or (res \ id 212 through 223 and (name N or name CA or name C or name O or name CB )) or r \ esid 224 or (resid 225 and (name N or name CA or name C or name O or name CB )) \ or resid 226 through 228 or (resid 229 through 233 and (name N or name CA or nam \ e C or name O or name CB )) or resid 234 or (resid 235 through 250 and (name N o \ r name CA or name C or name O or name CB )) or (resid 255 through 257 and (name \ N or name CA or name C or name O or name CB )) or resid 258 or (resid 259 throug \ h 267 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 21 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 38 or (resid 39 and (name N or nam \ e CA or name C or name O or name CB )) or resid 40 or (resid 41 through 42 and ( \ name N or name CA or name C or name O or name CB )) or (resid 43 through 48 and \ (name N or name CA or name C or name O or name CB )) or resid 49 or (resid 50 th \ rough 51 and (name N or name CA or name C or name O or name CB )) or resid 52 th \ rough 55 or (resid 56 through 57 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 58 through 61 and (name N or name CA or name C or name O or \ name CB )) or resid 62 through 66 or (resid 71 through 75 and (name N or name CA \ or name C or name O or name CB )) or resid 76 through 77 or (resid 78 through 8 \ 2 and (name N or name CA or name C or name O or name CB )) or (resid 83 through \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 through \ 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) or resi \ d 93 or (resid 94 through 99 and (name N or name CA or name C or name O or name \ CB )) or (resid 100 through 103 and (name N or name CA or name C or name O or na \ me CB )) or resid 104 or (resid 105 through 119 and (name N or name CA or name C \ or name O or name CB )) or resid 120 or (resid 121 through 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 132 or (resid 133 \ through 134 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 35 through 142 and (name N or name CA or name C or name O or name CB )) or resid \ 143 or (resid 144 through 152 and (name N or name CA or name C or name O or nam \ e CB )) or resid 153 or (resid 154 through 160 and (name N or name CA or name C \ or name O or name CB )) or resid 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB )) or resid 163 through 164 or (resid 165 and (name N o \ r name CA or name C or name O or name CB )) or resid 166 or (resid 167 through 1 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 169 or (res \ id 170 through 171 and (name N or name CA or name C or name O or name CB )) or r \ esid 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) \ or resid 174 through 175 or (resid 176 through 190 and (name N or name CA or nam \ e C or name O or name CB )) or resid 191 or (resid 192 through 211 and (name N o \ r name CA or name C or name O or name CB )) or (resid 212 through 217 and (name \ N or name CA or name C or name O or name CB )) or (resid 218 through 223 and (na \ me N or name CA or name C or name O or name CB )) or resid 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 228 o \ r (resid 229 through 233 and (name N or name CA or name C or name O or name CB ) \ ) or resid 234 or (resid 235 through 250 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 255 through 257 and (name N or name CA or name C or \ name O or name CB )) or resid 258 or (resid 259 through 267 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 21 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 40 or (resid 41 through 42 and (na \ me N or name CA or name C or name O or name CB )) or (resid 43 through 48 and (n \ ame N or name CA or name C or name O or name CB )) or resid 49 or (resid 50 thro \ ugh 51 and (name N or name CA or name C or name O or name CB )) or resid 52 or ( \ resid 53 through 57 and (name N or name CA or name C or name O or name CB )) or \ resid 58 or (resid 59 through 61 and (name N or name CA or name C or name O or n \ ame CB )) or resid 62 or (resid 63 through 66 and (name N or name CA or name C o \ r name O or name CB )) or (resid 71 through 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 77 or (resid 78 through 82 and (name \ N or name CA or name C or name O or name CB )) or (resid 83 through 87 and (nam \ e N or name CA or name C or name O or name CB )) or resid 88 through 89 or (resi \ d 90 and (name N or name CA or name C or name O or name CB )) or resid 91 or (re \ sid 92 and (name N or name CA or name C or name O or name CB )) or resid 93 or ( \ resid 94 through 99 and (name N or name CA or name C or name O or name CB )) or \ (resid 100 through 103 and (name N or name CA or name C or name O or name CB )) \ or resid 104 or (resid 105 through 119 and (name N or name CA or name C or name \ O or name CB )) or resid 120 through 122 or (resid 123 through 129 and (name N o \ r name CA or name C or name O or name CB )) or resid 130 through 131 or (resid 1 \ 32 through 134 and (name N or name CA or name C or name O or name CB )) or (resi \ d 135 through 142 and (name N or name CA or name C or name O or name CB )) or re \ sid 143 or (resid 144 through 152 and (name N or name CA or name C or name O or \ name CB )) or resid 153 through 161 or (resid 162 and (name N or name CA or name \ C or name O or name CB )) or resid 163 through 164 or (resid 165 and (name N or \ name CA or name C or name O or name CB )) or resid 166 or (resid 167 through 16 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 169 or (resi \ d 170 through 171 and (name N or name CA or name C or name O or name CB )) or re \ sid 172 through 175 or (resid 176 through 190 and (name N or name CA or name C o \ r name O or name CB )) or resid 191 or (resid 192 through 211 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 212 through 223 and (name N or \ name CA or name C or name O or name CB )) or resid 224 or (resid 225 and (name N \ or name CA or name C or name O or name CB )) or resid 226 through 228 or (resid \ 229 through 233 and (name N or name CA or name C or name O or name CB )) or (re \ sid 234 through 250 and (name N or name CA or name C or name O or name CB )) or \ (resid 255 through 267 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'E' and (resid 21 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and (na \ me N or name CA or name C or name O or name CB )) or resid 37 through 38 or (res \ id 39 and (name N or name CA or name C or name O or name CB )) or resid 40 or (r \ esid 41 through 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or \ resid 45 or (resid 46 through 48 and (name N or name CA or name C or name O or \ name CB )) or resid 49 or (resid 50 through 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 or (resid 53 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 or (resid 59 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 or (resid 63 throu \ gh 66 and (name N or name CA or name C or name O or name CB )) or (resid 71 thro \ ugh 75 and (name N or name CA or name C or name O or name CB )) or resid 76 thro \ ugh 77 or (resid 78 through 82 and (name N or name CA or name C or name O or nam \ e CB )) or resid 83 through 91 or (resid 92 and (name N or name CA or name C or \ name O or name CB )) or resid 93 or (resid 94 through 99 and (name N or name CA \ or name C or name O or name CB )) or (resid 100 through 103 and (name N or name \ CA or name C or name O or name CB )) or resid 104 or (resid 105 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 or (resid 121 \ through 129 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 0 through 131 or (resid 132 through 134 and (name N or name CA or name C or name \ O or name CB )) or (resid 135 through 142 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 143 through 152 and (name N or name CA or name C o \ r name O or name CB )) or resid 153 through 164 or (resid 165 and (name N or nam \ e CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 an \ d (name N or name CA or name C or name O or name CB )) or resid 169 or (resid 17 \ 0 through 171 and (name N or name CA or name C or name O or name CB )) or resid \ 172 through 175 or (resid 176 through 190 and (name N or name CA or name C or na \ me O or name CB )) or (resid 191 through 211 and (name N or name CA or name C or \ name O or name CB )) or (resid 212 through 223 and (name N or name CA or name C \ or name O or name CB )) or resid 224 or (resid 225 and (name N or name CA or na \ me C or name O or name CB )) or resid 226 through 228 or (resid 229 through 233 \ and (name N or name CA or name C or name O or name CB )) or (resid 234 through 2 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 258 through \ 267)) selection = (chain 'F' and ((resid 21 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 49 or (resid 50 through 51 and (n \ ame N or name CA or name C or name O or name CB )) or resid 52 through 62 or (re \ sid 63 through 75 and (name N or name CA or name C or name O or name CB )) or re \ sid 76 through 104 or (resid 105 through 119 and (name N or name CA or name C or \ name O or name CB )) or resid 120 or (resid 121 through 129 and (name N or name \ CA or name C or name O or name CB )) or resid 130 through 137 or (resid 138 thr \ ough 142 and (name N or name CA or name C or name O or name CB )) or resid 143 t \ hrough 164 or (resid 165 and (name N or name CA or name C or name O or name CB ) \ ) or resid 166 or (resid 167 through 168 and (name N or name CA or name C or nam \ e O or name CB )) or resid 169 through 176 or (resid 177 through 190 and (name N \ or name CA or name C or name O or name CB )) or (resid 191 through 211 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 212 through 223 and ( \ name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 through 233 and (name N or name CA or name C or name O or name CB )) \ or resid 234 through 250 or (resid 255 through 267 and (name N or name CA or nam \ e C or name O or name CB )))) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.560 Find NCS groups from input model: 0.410 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 0.035 11286 Z= 0.132 Angle : 0.548 5.848 15569 Z= 0.286 Chirality : 0.038 0.159 1943 Planarity : 0.003 0.038 2040 Dihedral : 10.727 85.179 3380 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.13 % Favored : 91.70 % Rotamer: Outliers : 0.16 % Allowed : 7.01 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.18 (0.22), residues: 1722 helix: 1.79 (0.20), residues: 771 sheet: -0.29 (0.30), residues: 308 loop : -1.81 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 222 TYR 0.008 0.001 TYR C 154 PHE 0.008 0.001 PHE B 169 TRP 0.013 0.002 TRP G 613 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00264 (11286) covalent geometry : angle 0.54771 (15569) hydrogen bonds : bond 0.15815 ( 606) hydrogen bonds : angle 5.91676 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.414 Fit side-chains REVERT: A 166 ARG cc_start: 0.9546 (ttm-80) cc_final: 0.9057 (ttp-110) REVERT: A 226 TYR cc_start: 0.9318 (m-10) cc_final: 0.9117 (m-80) REVERT: C 39 LYS cc_start: 0.8478 (pttt) cc_final: 0.8263 (pttt) REVERT: C 107 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8763 (mp10) REVERT: C 147 VAL cc_start: 0.9555 (t) cc_final: 0.9315 (m) REVERT: D 26 PHE cc_start: 0.9023 (t80) cc_final: 0.8752 (t80) REVERT: D 106 ASP cc_start: 0.9167 (t0) cc_final: 0.8874 (t70) REVERT: D 107 GLN cc_start: 0.9310 (mm-40) cc_final: 0.9056 (mm110) REVERT: E 112 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8431 (mtp85) REVERT: E 161 LEU cc_start: 0.8264 (mm) cc_final: 0.7731 (mp) REVERT: G 400 VAL cc_start: 0.9791 (t) cc_final: 0.9566 (p) REVERT: G 403 GLN cc_start: 0.8988 (mt0) cc_final: 0.8772 (mt0) REVERT: G 462 LEU cc_start: 0.9506 (tp) cc_final: 0.9235 (tt) REVERT: G 554 LEU cc_start: 0.9601 (tp) cc_final: 0.9401 (tp) REVERT: G 602 PHE cc_start: 0.8685 (t80) cc_final: 0.8128 (t80) REVERT: G 641 ARG cc_start: 0.9678 (ttp-170) cc_final: 0.9349 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.0985 time to fit residues: 29.2872 Evaluate side-chains 132 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 107 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.048011 restraints weight = 59331.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.048543 restraints weight = 43809.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048812 restraints weight = 34115.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049042 restraints weight = 30080.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049080 restraints weight = 29076.042| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11286 Z= 0.169 Angle : 0.614 8.109 15569 Z= 0.298 Chirality : 0.040 0.147 1943 Planarity : 0.004 0.040 2040 Dihedral : 8.432 83.531 1958 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.42 % Favored : 91.41 % Rotamer: Outliers : 2.96 % Allowed : 14.80 % Favored : 82.24 % 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: 0.17 (0.22), residues: 1722 helix: 1.75 (0.19), residues: 804 sheet: -0.26 (0.31), residues: 296 loop : -1.95 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 166 TYR 0.015 0.001 TYR A 104 PHE 0.012 0.001 PHE C 49 TRP 0.014 0.002 TRP G 613 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00352 (11286) covalent geometry : angle 0.61376 (15569) hydrogen bonds : bond 0.02920 ( 606) hydrogen bonds : angle 4.67942 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9530 (ttm-80) cc_final: 0.9081 (ttp-110) REVERT: A 226 TYR cc_start: 0.9312 (m-10) cc_final: 0.8992 (m-80) REVERT: C 107 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8709 (mp10) REVERT: C 145 MET cc_start: 0.8248 (mtp) cc_final: 0.7984 (mmm) REVERT: D 105 LEU cc_start: 0.9390 (mp) cc_final: 0.8890 (tt) REVERT: D 106 ASP cc_start: 0.9070 (t0) cc_final: 0.8857 (t70) REVERT: D 107 GLN cc_start: 0.9357 (mm-40) cc_final: 0.9013 (mm110) REVERT: E 112 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8493 (ttm110) REVERT: E 226 TYR cc_start: 0.9142 (m-10) cc_final: 0.8900 (m-10) REVERT: F 52 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8548 (t70) REVERT: G 400 VAL cc_start: 0.9830 (t) cc_final: 0.9619 (p) REVERT: G 403 GLN cc_start: 0.9034 (mt0) cc_final: 0.8816 (mt0) REVERT: G 462 LEU cc_start: 0.9543 (tp) cc_final: 0.9303 (tt) REVERT: G 602 PHE cc_start: 0.8720 (t80) cc_final: 0.8016 (t80) REVERT: G 641 ARG cc_start: 0.9710 (ttp-170) cc_final: 0.9413 (ttp-110) outliers start: 19 outliers final: 9 residues processed: 164 average time/residue: 0.0920 time to fit residues: 22.7967 Evaluate side-chains 146 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 45 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 98 optimal weight: 0.0370 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN B 151 ASN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.047245 restraints weight = 59935.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047754 restraints weight = 45688.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048066 restraints weight = 37909.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048212 restraints weight = 33307.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.048343 restraints weight = 31380.485| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11286 Z= 0.189 Angle : 0.618 8.028 15569 Z= 0.302 Chirality : 0.039 0.141 1943 Planarity : 0.004 0.044 2040 Dihedral : 8.582 83.024 1958 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.77 % Favored : 91.06 % Rotamer: Outliers : 4.21 % Allowed : 14.33 % Favored : 81.46 % 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: 0.08 (0.21), residues: 1722 helix: 1.66 (0.19), residues: 805 sheet: -0.31 (0.31), residues: 294 loop : -1.97 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 166 TYR 0.020 0.001 TYR G 640 PHE 0.018 0.001 PHE F 26 TRP 0.015 0.002 TRP G 613 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00390 (11286) covalent geometry : angle 0.61774 (15569) hydrogen bonds : bond 0.02896 ( 606) hydrogen bonds : angle 4.58210 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9590 (ttm-80) cc_final: 0.9093 (ttp-110) REVERT: A 226 TYR cc_start: 0.9323 (m-10) cc_final: 0.8935 (m-80) REVERT: C 39 LYS cc_start: 0.8363 (pttt) cc_final: 0.7315 (pttt) REVERT: C 107 GLN cc_start: 0.9253 (mm-40) cc_final: 0.8740 (mp10) REVERT: D 16 TYR cc_start: 0.7944 (t80) cc_final: 0.7734 (t80) REVERT: D 105 LEU cc_start: 0.9375 (mp) cc_final: 0.8851 (tt) REVERT: D 107 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9109 (mm110) REVERT: E 102 ILE cc_start: 0.8805 (mp) cc_final: 0.8601 (mp) REVERT: E 112 ARG cc_start: 0.9019 (mtp85) cc_final: 0.8283 (mtp85) REVERT: E 226 TYR cc_start: 0.9259 (m-10) cc_final: 0.8915 (m-10) REVERT: E 245 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8647 (tmm) REVERT: F 52 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8543 (t70) REVERT: G 403 GLN cc_start: 0.9065 (mt0) cc_final: 0.8843 (mt0) REVERT: G 462 LEU cc_start: 0.9553 (tp) cc_final: 0.9290 (tt) REVERT: G 602 PHE cc_start: 0.8754 (t80) cc_final: 0.8122 (t80) REVERT: G 641 ARG cc_start: 0.9716 (ttp-170) cc_final: 0.9422 (ttp-110) outliers start: 27 outliers final: 17 residues processed: 157 average time/residue: 0.0919 time to fit residues: 21.8386 Evaluate side-chains 153 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 chunk 171 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN D 30 HIS D 52 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.057860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049201 restraints weight = 58488.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049624 restraints weight = 43253.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049982 restraints weight = 36517.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050102 restraints weight = 32998.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.050255 restraints weight = 31731.505| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11286 Z= 0.088 Angle : 0.573 7.081 15569 Z= 0.271 Chirality : 0.039 0.136 1943 Planarity : 0.003 0.041 2040 Dihedral : 7.950 84.253 1958 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.08 % Favored : 92.74 % Rotamer: Outliers : 2.49 % Allowed : 18.07 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.22), residues: 1722 helix: 2.05 (0.19), residues: 791 sheet: -0.10 (0.31), residues: 296 loop : -1.84 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 166 TYR 0.014 0.001 TYR D 150 PHE 0.019 0.001 PHE C 49 TRP 0.010 0.001 TRP G 613 HIS 0.003 0.000 HIS G 599 Details of bonding type rmsd covalent geometry : bond 0.00201 (11286) covalent geometry : angle 0.57292 (15569) hydrogen bonds : bond 0.02048 ( 606) hydrogen bonds : angle 4.10479 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9538 (ttm-80) cc_final: 0.9046 (ttp-110) REVERT: A 226 TYR cc_start: 0.9328 (m-10) cc_final: 0.8946 (m-80) REVERT: C 107 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8953 (mp10) REVERT: C 207 LEU cc_start: 0.9488 (mt) cc_final: 0.9204 (pp) REVERT: C 246 ILE cc_start: 0.9338 (mm) cc_final: 0.9072 (mp) REVERT: E 112 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8379 (ttm110) REVERT: E 167 GLN cc_start: 0.9363 (mt0) cc_final: 0.8880 (mp10) REVERT: E 226 TYR cc_start: 0.9233 (m-10) cc_final: 0.8854 (m-10) REVERT: E 245 MET cc_start: 0.9090 (ttp) cc_final: 0.8651 (tmm) REVERT: F 52 HIS cc_start: 0.8932 (OUTLIER) cc_final: 0.8666 (t70) REVERT: G 403 GLN cc_start: 0.9001 (mt0) cc_final: 0.8734 (mt0) REVERT: G 462 LEU cc_start: 0.9521 (tp) cc_final: 0.9242 (tt) REVERT: G 602 PHE cc_start: 0.8861 (t80) cc_final: 0.8444 (t80) REVERT: G 641 ARG cc_start: 0.9683 (ttp-170) cc_final: 0.9446 (ttp-110) outliers start: 16 outliers final: 10 residues processed: 170 average time/residue: 0.0922 time to fit residues: 23.3590 Evaluate side-chains 152 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 52 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.055077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047053 restraints weight = 60617.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047656 restraints weight = 44655.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047802 restraints weight = 35378.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048143 restraints weight = 32492.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.048131 restraints weight = 29688.764| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11286 Z= 0.232 Angle : 0.665 7.384 15569 Z= 0.325 Chirality : 0.040 0.139 1943 Planarity : 0.004 0.045 2040 Dihedral : 8.739 82.680 1958 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.89 % Favored : 90.94 % Rotamer: Outliers : 4.21 % Allowed : 18.22 % Favored : 77.57 % 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: 0.19 (0.22), residues: 1722 helix: 1.75 (0.19), residues: 805 sheet: -0.19 (0.32), residues: 294 loop : -1.95 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 222 TYR 0.023 0.002 TYR A 104 PHE 0.014 0.001 PHE B 49 TRP 0.019 0.002 TRP D 88 HIS 0.008 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00469 (11286) covalent geometry : angle 0.66523 (15569) hydrogen bonds : bond 0.02966 ( 606) hydrogen bonds : angle 4.62028 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9586 (ttm-80) cc_final: 0.9048 (ttp-110) REVERT: A 226 TYR cc_start: 0.9378 (m-10) cc_final: 0.9020 (m-80) REVERT: B 150 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8070 (p90) REVERT: C 107 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8732 (mp10) REVERT: E 112 ARG cc_start: 0.9022 (mtp85) cc_final: 0.8403 (ttm110) REVERT: E 245 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8682 (tmm) REVERT: F 52 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8544 (t70) REVERT: G 403 GLN cc_start: 0.9129 (mt0) cc_final: 0.8809 (mt0) REVERT: G 462 LEU cc_start: 0.9577 (tp) cc_final: 0.9320 (tt) REVERT: G 602 PHE cc_start: 0.8836 (t80) cc_final: 0.8318 (t80) REVERT: G 641 ARG cc_start: 0.9715 (ttp-170) cc_final: 0.9453 (ttp-110) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.0955 time to fit residues: 20.9895 Evaluate side-chains 150 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 150 TYR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 157 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047306 restraints weight = 59779.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047818 restraints weight = 44789.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048161 restraints weight = 35874.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048162 restraints weight = 31418.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048161 restraints weight = 31411.625| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11286 Z= 0.171 Angle : 0.623 7.339 15569 Z= 0.302 Chirality : 0.040 0.136 1943 Planarity : 0.004 0.062 2040 Dihedral : 8.589 83.286 1958 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.42 % Favored : 91.41 % Rotamer: Outliers : 3.12 % Allowed : 20.40 % Favored : 76.48 % 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: 0.23 (0.22), residues: 1722 helix: 1.79 (0.19), residues: 803 sheet: -0.17 (0.32), residues: 294 loop : -1.94 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 126 TYR 0.016 0.001 TYR D 150 PHE 0.008 0.001 PHE C 49 TRP 0.013 0.002 TRP D 88 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00357 (11286) covalent geometry : angle 0.62328 (15569) hydrogen bonds : bond 0.02560 ( 606) hydrogen bonds : angle 4.42785 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9562 (ttm-80) cc_final: 0.9046 (ttp-110) REVERT: A 226 TYR cc_start: 0.9362 (m-10) cc_final: 0.8988 (m-80) REVERT: C 107 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8973 (mp10) REVERT: C 207 LEU cc_start: 0.9491 (mt) cc_final: 0.9199 (pp) REVERT: D 107 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9084 (mm-40) REVERT: E 112 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8347 (mtp85) REVERT: E 226 TYR cc_start: 0.9248 (m-10) cc_final: 0.8908 (m-10) REVERT: E 245 MET cc_start: 0.9092 (ttp) cc_final: 0.8699 (tmm) REVERT: F 52 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.8569 (t70) REVERT: G 403 GLN cc_start: 0.9118 (mt0) cc_final: 0.8811 (mt0) REVERT: G 462 LEU cc_start: 0.9551 (tp) cc_final: 0.9281 (tt) REVERT: G 602 PHE cc_start: 0.8865 (t80) cc_final: 0.8341 (t80) REVERT: G 641 ARG cc_start: 0.9714 (ttp-170) cc_final: 0.9458 (ttp-110) outliers start: 20 outliers final: 15 residues processed: 147 average time/residue: 0.0855 time to fit residues: 19.1891 Evaluate side-chains 146 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 162 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 169 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048542 restraints weight = 58473.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.049110 restraints weight = 43156.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049341 restraints weight = 33815.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049341 restraints weight = 30443.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.049341 restraints weight = 30441.648| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.002 0.040 11286 Z= 0.107 Angle : 0.602 8.798 15569 Z= 0.284 Chirality : 0.039 0.150 1943 Planarity : 0.003 0.041 2040 Dihedral : 8.224 83.405 1958 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.96 % Favored : 91.87 % Rotamer: Outliers : 2.18 % Allowed : 21.65 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1722 helix: 2.03 (0.20), residues: 798 sheet: -0.04 (0.32), residues: 294 loop : -1.80 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 126 TYR 0.016 0.001 TYR D 150 PHE 0.020 0.001 PHE C 49 TRP 0.009 0.001 TRP G 613 HIS 0.003 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00241 (11286) covalent geometry : angle 0.60221 (15569) hydrogen bonds : bond 0.02180 ( 606) hydrogen bonds : angle 4.17527 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9538 (ttm-80) cc_final: 0.9053 (ttp-110) REVERT: A 226 TYR cc_start: 0.9349 (m-10) cc_final: 0.8968 (m-80) REVERT: C 107 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8752 (mp10) REVERT: C 207 LEU cc_start: 0.9469 (mt) cc_final: 0.9189 (pp) REVERT: C 245 MET cc_start: 0.8290 (mmt) cc_final: 0.7750 (mmt) REVERT: E 112 ARG cc_start: 0.8984 (mtp85) cc_final: 0.8351 (mtp85) REVERT: E 226 TYR cc_start: 0.9229 (m-10) cc_final: 0.8886 (m-10) REVERT: E 245 MET cc_start: 0.9086 (ttp) cc_final: 0.8704 (tmm) REVERT: F 52 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8605 (t70) REVERT: G 403 GLN cc_start: 0.9053 (mt0) cc_final: 0.8774 (mt0) REVERT: G 462 LEU cc_start: 0.9519 (tp) cc_final: 0.9225 (tt) REVERT: G 602 PHE cc_start: 0.8924 (t80) cc_final: 0.8555 (t80) REVERT: G 641 ARG cc_start: 0.9705 (ttp-170) cc_final: 0.9457 (ttp-110) outliers start: 14 outliers final: 12 residues processed: 149 average time/residue: 0.0877 time to fit residues: 19.7395 Evaluate side-chains 151 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 636 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 124 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 0.0570 chunk 147 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.056713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.048382 restraints weight = 58437.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.048994 restraints weight = 43815.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049456 restraints weight = 35322.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049448 restraints weight = 31052.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049450 restraints weight = 29872.732| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11286 Z= 0.123 Angle : 0.604 7.927 15569 Z= 0.288 Chirality : 0.039 0.137 1943 Planarity : 0.003 0.041 2040 Dihedral : 8.238 82.516 1958 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.84 % Favored : 91.99 % Rotamer: Outliers : 2.49 % Allowed : 22.59 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.22), residues: 1722 helix: 2.06 (0.20), residues: 798 sheet: 0.01 (0.32), residues: 294 loop : -1.75 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 126 TYR 0.024 0.001 TYR F 104 PHE 0.019 0.001 PHE B 49 TRP 0.009 0.001 TRP G 613 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00269 (11286) covalent geometry : angle 0.60405 (15569) hydrogen bonds : bond 0.02202 ( 606) hydrogen bonds : angle 4.17215 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9582 (ttm-80) cc_final: 0.9042 (ttp-110) REVERT: A 226 TYR cc_start: 0.9364 (m-10) cc_final: 0.9020 (m-80) REVERT: C 107 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8789 (mp10) REVERT: C 207 LEU cc_start: 0.9478 (mt) cc_final: 0.9178 (pp) REVERT: C 245 MET cc_start: 0.8318 (mmt) cc_final: 0.7821 (mmt) REVERT: E 112 ARG cc_start: 0.8972 (mtp85) cc_final: 0.8351 (mtp85) REVERT: E 226 TYR cc_start: 0.9244 (m-10) cc_final: 0.8893 (m-10) REVERT: E 245 MET cc_start: 0.9094 (ttp) cc_final: 0.8706 (tmm) REVERT: G 403 GLN cc_start: 0.9097 (mt0) cc_final: 0.8774 (mt0) REVERT: G 462 LEU cc_start: 0.9535 (tp) cc_final: 0.9244 (tt) REVERT: G 602 PHE cc_start: 0.8937 (t80) cc_final: 0.8542 (t80) REVERT: G 641 ARG cc_start: 0.9709 (ttp-170) cc_final: 0.9456 (ttp-110) outliers start: 16 outliers final: 13 residues processed: 149 average time/residue: 0.0930 time to fit residues: 20.4075 Evaluate side-chains 147 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 16 optimal weight: 9.9990 chunk 50 optimal weight: 0.2980 chunk 171 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049100 restraints weight = 57645.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.049638 restraints weight = 41504.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049897 restraints weight = 34424.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049901 restraints weight = 30367.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049901 restraints weight = 30347.933| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11286 Z= 0.106 Angle : 0.614 9.242 15569 Z= 0.288 Chirality : 0.039 0.148 1943 Planarity : 0.003 0.040 2040 Dihedral : 8.070 82.946 1958 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.38 % Favored : 92.45 % Rotamer: Outliers : 2.34 % Allowed : 23.21 % Favored : 74.45 % 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: 0.61 (0.22), residues: 1722 helix: 2.11 (0.19), residues: 798 sheet: -0.05 (0.32), residues: 304 loop : -1.71 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.020 0.001 TYR A 104 PHE 0.037 0.001 PHE D 49 TRP 0.009 0.001 TRP G 613 HIS 0.003 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00242 (11286) covalent geometry : angle 0.61394 (15569) hydrogen bonds : bond 0.02066 ( 606) hydrogen bonds : angle 4.08432 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9550 (ttm-80) cc_final: 0.9049 (ttp-110) REVERT: A 226 TYR cc_start: 0.9346 (m-10) cc_final: 0.9015 (m-80) REVERT: C 107 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8781 (mp10) REVERT: C 207 LEU cc_start: 0.9446 (mt) cc_final: 0.9157 (pp) REVERT: C 245 MET cc_start: 0.8346 (mmt) cc_final: 0.7941 (mmt) REVERT: E 112 ARG cc_start: 0.8959 (mtp85) cc_final: 0.8346 (mtp85) REVERT: E 226 TYR cc_start: 0.9225 (m-10) cc_final: 0.8872 (m-10) REVERT: E 245 MET cc_start: 0.9079 (ttp) cc_final: 0.8646 (tmm) REVERT: F 166 ARG cc_start: 0.9296 (ttm-80) cc_final: 0.8763 (ttt90) REVERT: G 403 GLN cc_start: 0.9087 (mt0) cc_final: 0.8744 (mt0) REVERT: G 462 LEU cc_start: 0.9524 (tp) cc_final: 0.9224 (tt) REVERT: G 602 PHE cc_start: 0.8933 (t80) cc_final: 0.8599 (t80) REVERT: G 641 ARG cc_start: 0.9707 (ttp-170) cc_final: 0.9459 (ttp-110) outliers start: 15 outliers final: 13 residues processed: 145 average time/residue: 0.0953 time to fit residues: 20.6399 Evaluate side-chains 147 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 0.6980 chunk 48 optimal weight: 0.0570 chunk 160 optimal weight: 20.0000 chunk 138 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.057491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048988 restraints weight = 58890.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.049525 restraints weight = 42475.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049737 restraints weight = 35293.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049737 restraints weight = 31508.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049737 restraints weight = 31508.497| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11286 Z= 0.116 Angle : 0.613 9.699 15569 Z= 0.290 Chirality : 0.039 0.151 1943 Planarity : 0.003 0.040 2040 Dihedral : 8.091 82.381 1958 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.67 % Favored : 92.16 % Rotamer: Outliers : 2.02 % Allowed : 23.52 % Favored : 74.45 % 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: 0.64 (0.22), residues: 1722 helix: 2.14 (0.19), residues: 798 sheet: -0.06 (0.32), residues: 304 loop : -1.70 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 126 TYR 0.024 0.001 TYR F 104 PHE 0.021 0.001 PHE A 26 TRP 0.009 0.001 TRP G 613 HIS 0.004 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00260 (11286) covalent geometry : angle 0.61307 (15569) hydrogen bonds : bond 0.02111 ( 606) hydrogen bonds : angle 4.09196 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.9558 (ttm-80) cc_final: 0.9042 (ttp-110) REVERT: A 226 TYR cc_start: 0.9358 (m-10) cc_final: 0.9018 (m-80) REVERT: C 107 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8769 (mp10) REVERT: C 207 LEU cc_start: 0.9469 (mt) cc_final: 0.9173 (pp) REVERT: C 245 MET cc_start: 0.8370 (mmt) cc_final: 0.7970 (mmt) REVERT: E 112 ARG cc_start: 0.8965 (mtp85) cc_final: 0.8464 (ttm110) REVERT: E 226 TYR cc_start: 0.9234 (m-10) cc_final: 0.8870 (m-10) REVERT: E 245 MET cc_start: 0.9072 (ttp) cc_final: 0.8607 (tmm) REVERT: F 166 ARG cc_start: 0.9281 (ttm-80) cc_final: 0.8755 (ttt90) REVERT: G 403 GLN cc_start: 0.9109 (mt0) cc_final: 0.8747 (mt0) REVERT: G 462 LEU cc_start: 0.9534 (tp) cc_final: 0.9238 (tt) REVERT: G 602 PHE cc_start: 0.8962 (t80) cc_final: 0.8639 (t80) REVERT: G 641 ARG cc_start: 0.9709 (ttp-170) cc_final: 0.9453 (ttp-110) outliers start: 13 outliers final: 13 residues processed: 143 average time/residue: 0.0928 time to fit residues: 19.7267 Evaluate side-chains 145 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 52 HIS Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain G residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 27 optimal weight: 0.0070 chunk 55 optimal weight: 0.0570 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 389 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050455 restraints weight = 57846.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050869 restraints weight = 42418.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051194 restraints weight = 35944.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051194 restraints weight = 32089.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051194 restraints weight = 32089.477| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11286 Z= 0.094 Angle : 0.614 8.889 15569 Z= 0.287 Chirality : 0.039 0.136 1943 Planarity : 0.003 0.038 2040 Dihedral : 7.609 85.084 1958 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.45 % Favored : 93.38 % Rotamer: Outliers : 1.25 % Allowed : 23.99 % Favored : 74.77 % 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: 0.75 (0.22), residues: 1722 helix: 2.23 (0.19), residues: 798 sheet: 0.04 (0.32), residues: 299 loop : -1.66 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 126 TYR 0.022 0.001 TYR A 104 PHE 0.023 0.001 PHE C 49 TRP 0.009 0.001 TRP G 613 HIS 0.003 0.000 HIS G 599 Details of bonding type rmsd covalent geometry : bond 0.00217 (11286) covalent geometry : angle 0.61393 (15569) hydrogen bonds : bond 0.01766 ( 606) hydrogen bonds : angle 3.93617 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.73 seconds wall clock time: 29 minutes 2.86 seconds (1742.86 seconds total)