Starting phenix.real_space_refine on Mon Jun 9 06:19:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxr_27774/06_2025/8dxr_27774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxr_27774/06_2025/8dxr_27774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dxr_27774/06_2025/8dxr_27774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxr_27774/06_2025/8dxr_27774.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxr_27774/06_2025/8dxr_27774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxr_27774/06_2025/8dxr_27774.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 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: 3 Type Number sf(0) Gaussians C 6233 2.51 5 N 2101 2.21 5 O 2101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10435 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 1480 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1071 Unresolved non-hydrogen angles: 1377 Unresolved non-hydrogen dihedrals: 935 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 16, 'PHE:plan': 25, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 597 Chain: "B" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 1490 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1081 Unresolved non-hydrogen angles: 1388 Unresolved non-hydrogen dihedrals: 944 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 25, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 600 Chain: "C" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 1495 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 278} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1082 Unresolved non-hydrogen angles: 1389 Unresolved non-hydrogen dihedrals: 945 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 25, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 600 Chain: "D" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 1490 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 7, 'TRANS': 292} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1386 Unresolved non-hydrogen dihedrals: 941 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 16, 'PHE:plan': 25, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 601 Chain: "E" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 1495 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 278} Link IDs: {'PTRANS': 7, 'TRANS': 293} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1082 Unresolved non-hydrogen angles: 1389 Unresolved non-hydrogen dihedrals: 945 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 25, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 600 Chain: "F" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 1500 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 279} Link IDs: {'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1086 Unresolved non-hydrogen angles: 1394 Unresolved non-hydrogen dihedrals: 948 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 17, 'PHE:plan': 25, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 604 Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 1485 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 7, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1075 Unresolved non-hydrogen angles: 1382 Unresolved non-hydrogen dihedrals: 938 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 7, 'TYR:plan': 19, 'ASN:plan1': 9, 'TRP:plan': 6, 'ASP:plan': 16, 'PHE:plan': 25, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 601 Time building chain proxies: 9.41, per 1000 atoms: 0.90 Number of scatterers: 10435 At special positions: 0 Unit cell: (111.1, 114.4, 127.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2101 8.00 N 2101 7.00 C 6233 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: 3.34 Conformation dependent library (CDL) restraints added in 2.2 seconds 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4062 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 7 sheets defined 69.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 26 through 48 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 126 through 147 removed outlier: 3.558A pdb=" N TRP A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N PHE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.898A pdb=" N ILE A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.638A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 253 Processing helix chain 'A' and resid 261 through 283 removed outlier: 3.693A pdb=" N ALA A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 341 removed outlier: 4.623A pdb=" N SER A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.878A pdb=" N GLN A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 3.554A pdb=" N ARG A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.923A pdb=" N GLU A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 48 removed outlier: 4.770A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.506A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 140 removed outlier: 3.962A pdb=" N TYR B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Proline residue: B 128 - end of helix Processing helix chain 'B' and resid 151 through 165 removed outlier: 3.838A pdb=" N ILE B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 232 through 252 Processing helix chain 'B' and resid 260 through 283 removed outlier: 3.885A pdb=" N LEU B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 341 Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 381 removed outlier: 4.059A pdb=" N GLN B 379 " --> pdb=" O HIS B 375 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.585A pdb=" N ARG B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.711A pdb=" N LEU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 48 removed outlier: 3.554A pdb=" N PHE C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 119 removed outlier: 4.693A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 143 removed outlier: 3.657A pdb=" N LEU C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 131 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 143 " --> pdb=" O MET C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.511A pdb=" N ASP C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 Processing helix chain 'C' and resid 232 through 252 Processing helix chain 'C' and resid 260 through 283 removed outlier: 3.637A pdb=" N ARG C 264 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 313 through 341 removed outlier: 3.910A pdb=" N LYS C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 368 through 378 Processing helix chain 'C' and resid 383 through 391 removed outlier: 4.335A pdb=" N PHE C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 Processing helix chain 'D' and resid 22 through 47 Processing helix chain 'D' and resid 104 through 116 Processing helix chain 'D' and resid 126 through 141 removed outlier: 3.772A pdb=" N LEU D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 148 through 166 removed outlier: 4.322A pdb=" N SER D 153 " --> pdb=" O PRO D 149 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 176 removed outlier: 3.828A pdb=" N THR D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.698A pdb=" N LYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.708A pdb=" N MET D 261 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 257 through 262' Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.997A pdb=" N LEU D 283 " --> pdb=" O TYR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 314 removed outlier: 4.531A pdb=" N HIS D 314 " --> pdb=" O THR D 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 315 through 344 removed outlier: 3.649A pdb=" N PHE D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 359 Processing helix chain 'D' and resid 367 through 381 Processing helix chain 'D' and resid 383 through 390 removed outlier: 3.519A pdb=" N VAL D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 405 removed outlier: 3.597A pdb=" N LEU D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 removed outlier: 4.530A pdb=" N VAL E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS E 21 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 49 Processing helix chain 'E' and resid 106 through 119 removed outlier: 4.773A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.932A pdb=" N TYR E 126 " --> pdb=" O TRP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 142 removed outlier: 3.872A pdb=" N LEU E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 131 " --> pdb=" O PHE E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 148 removed outlier: 3.662A pdb=" N LYS E 147 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE E 148 " --> pdb=" O TRP E 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 148' Processing helix chain 'E' and resid 152 through 167 removed outlier: 4.397A pdb=" N PHE E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 176 removed outlier: 4.364A pdb=" N THR E 172 " --> pdb=" O SER E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 Processing helix chain 'E' and resid 259 through 283 removed outlier: 3.684A pdb=" N LEU E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 344 removed outlier: 3.865A pdb=" N ARG E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 359 removed outlier: 3.511A pdb=" N ARG E 355 " --> pdb=" O PHE E 351 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 381 removed outlier: 4.209A pdb=" N GLN E 379 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR E 380 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 393 through 405 removed outlier: 3.943A pdb=" N GLU E 397 " --> pdb=" O SER E 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 49 removed outlier: 3.836A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 119 removed outlier: 3.643A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 126 through 143 removed outlier: 4.197A pdb=" N LEU F 130 " --> pdb=" O TYR F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 167 removed outlier: 4.029A pdb=" N ILE F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 176 Processing helix chain 'F' and resid 232 through 253 removed outlier: 3.759A pdb=" N LEU F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 283 removed outlier: 3.929A pdb=" N SER F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 342 removed outlier: 3.504A pdb=" N TYR F 330 " --> pdb=" O PHE F 326 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 358 removed outlier: 4.249A pdb=" N ARG F 355 " --> pdb=" O PHE F 351 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 378 removed outlier: 3.500A pdb=" N ALA F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 393 through 405 Processing helix chain 'G' and resid 16 through 20 removed outlier: 4.132A pdb=" N VAL G 19 " --> pdb=" O ALA G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 49 removed outlier: 3.956A pdb=" N VAL G 26 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.861A pdb=" N TYR G 108 " --> pdb=" O ASP G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.688A pdb=" N LYS G 125 " --> pdb=" O HIS G 121 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR G 126 " --> pdb=" O TRP G 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 121 through 126' Processing helix chain 'G' and resid 126 through 142 removed outlier: 3.808A pdb=" N LEU G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 165 removed outlier: 3.631A pdb=" N GLU G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 235 through 253 Processing helix chain 'G' and resid 257 through 283 removed outlier: 3.937A pdb=" N MET G 261 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL G 263 " --> pdb=" O TYR G 259 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER G 281 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 340 removed outlier: 3.621A pdb=" N PHE G 316 " --> pdb=" O MET G 312 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LYS G 318 " --> pdb=" O HIS G 314 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE G 321 " --> pdb=" O SER G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 359 Processing helix chain 'G' and resid 367 through 378 Processing helix chain 'G' and resid 379 through 381 No H-bonds generated for 'chain 'G' and resid 379 through 381' Processing helix chain 'G' and resid 382 through 390 removed outlier: 3.882A pdb=" N LYS G 386 " --> pdb=" O PRO G 382 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL G 390 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 removed outlier: 4.261A pdb=" N ASN F 309 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 55 through 56 1021 hydrogen bonds defined for protein. 3015 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: 3.64 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 2101 1.28 - 1.35: 2080 1.35 - 1.41: 0 1.41 - 1.48: 2101 1.48 - 1.54: 4132 Bond restraints: 10414 Sorted by residual: bond pdb=" CA GLN A 46 " pdb=" C GLN A 46 " ideal model delta sigma weight residual 1.522 1.491 0.032 1.40e-02 5.10e+03 5.14e+00 bond pdb=" C MET C 300 " pdb=" N THR C 301 " ideal model delta sigma weight residual 1.331 1.305 0.026 1.40e-02 5.10e+03 3.57e+00 bond pdb=" C PHE G 316 " pdb=" N SER G 317 " ideal model delta sigma weight residual 1.333 1.305 0.028 1.73e-02 3.34e+03 2.58e+00 bond pdb=" CA VAL A 291 " pdb=" CB VAL A 291 " ideal model delta sigma weight residual 1.551 1.534 0.017 1.08e-02 8.57e+03 2.38e+00 bond pdb=" N ILE B 52 " pdb=" CA ILE B 52 " ideal model delta sigma weight residual 1.456 1.439 0.018 1.19e-02 7.06e+03 2.18e+00 ... (remaining 10409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 14478 4.28 - 8.55: 24 8.55 - 12.83: 1 12.83 - 17.11: 0 17.11 - 21.38: 1 Bond angle restraints: 14504 Sorted by residual: angle pdb=" N GLY E 150 " pdb=" CA GLY E 150 " pdb=" C GLY E 150 " ideal model delta sigma weight residual 113.18 91.80 21.38 2.37e+00 1.78e-01 8.14e+01 angle pdb=" N PRO E 149 " pdb=" CA PRO E 149 " pdb=" C PRO E 149 " ideal model delta sigma weight residual 112.47 100.19 12.28 2.06e+00 2.36e-01 3.56e+01 angle pdb=" N ILE E 257 " pdb=" CA ILE E 257 " pdb=" C ILE E 257 " ideal model delta sigma weight residual 113.20 108.08 5.12 9.60e-01 1.09e+00 2.85e+01 angle pdb=" N TYR B 259 " pdb=" CA TYR B 259 " pdb=" C TYR B 259 " ideal model delta sigma weight residual 112.88 106.01 6.87 1.29e+00 6.01e-01 2.83e+01 angle pdb=" C ASN B 368 " pdb=" CA ASN B 368 " pdb=" CB ASN B 368 " ideal model delta sigma weight residual 117.23 110.05 7.18 1.36e+00 5.41e-01 2.79e+01 ... (remaining 14499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.35: 5632 5.35 - 10.70: 399 10.70 - 16.04: 81 16.04 - 21.39: 26 21.39 - 26.74: 4 Dihedral angle restraints: 6142 sinusoidal: 0 harmonic: 6142 Sorted by residual: dihedral pdb=" CA HIS G 314 " pdb=" C HIS G 314 " pdb=" N LEU G 315 " pdb=" CA LEU G 315 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE G 289 " pdb=" C PHE G 289 " pdb=" N THR G 290 " pdb=" CA THR G 290 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PHE A 316 " pdb=" C PHE A 316 " pdb=" N SER A 317 " pdb=" CA SER A 317 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 6139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1179 0.035 - 0.071: 677 0.071 - 0.106: 144 0.106 - 0.142: 25 0.142 - 0.177: 6 Chirality restraints: 2031 Sorted by residual: chirality pdb=" CA ILE A 297 " pdb=" N ILE A 297 " pdb=" C ILE A 297 " pdb=" CB ILE A 297 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA PRO E 149 " pdb=" N PRO E 149 " pdb=" C PRO E 149 " pdb=" CB PRO E 149 " both_signs ideal model delta sigma weight residual False 2.72 2.89 -0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE C 297 " pdb=" N ILE C 297 " pdb=" C ILE C 297 " pdb=" CB ILE C 297 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 2028 not shown) Planarity restraints: 2080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 324 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" C LEU E 324 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU E 324 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS E 325 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 315 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C LEU A 315 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 315 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 316 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 330 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C TYR F 330 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR F 330 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY F 331 " -0.011 2.00e-02 2.50e+03 ... (remaining 2077 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4239 2.86 - 3.37: 10542 3.37 - 3.88: 15351 3.88 - 4.39: 14120 4.39 - 4.90: 23720 Nonbonded interactions: 67972 Sorted by model distance: nonbonded pdb=" O ARG E 347 " pdb=" N ASN E 368 " model vdw 2.348 3.120 nonbonded pdb=" O TYR C 123 " pdb=" N TYR C 126 " model vdw 2.355 3.120 nonbonded pdb=" O LEU C 283 " pdb=" N LYS C 286 " model vdw 2.386 3.120 nonbonded pdb=" O GLU A 234 " pdb=" N ALA A 238 " model vdw 2.389 3.120 nonbonded pdb=" O VAL D 252 " pdb=" N GLU D 254 " model vdw 2.389 3.120 ... (remaining 67967 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 16 through 175 or resid 234 through 405)) selection = (chain 'B' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'C' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'D' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'E' and (resid 16 through 175 or resid 234 through 405)) selection = (chain 'F' and (resid 16 through 175 or resid 177 or resid 235 through 405)) selection = (chain 'G' and (resid 16 through 175 or resid 177 or resid 235 through 405)) } 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.490 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.004 0.032 10414 Z= 0.270 Angle : 0.807 21.384 14504 Z= 0.549 Chirality : 0.043 0.177 2031 Planarity : 0.004 0.020 2080 Dihedral : 5.274 26.738 2080 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.56 % Favored : 88.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 2059 helix: 1.08 (0.14), residues: 1318 sheet: -2.37 (0.44), residues: 112 loop : -3.83 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.15218 ( 1021) hydrogen bonds : angle 6.40054 ( 3015) covalent geometry : bond 0.00363 (10414) covalent geometry : angle 0.80720 (14504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0934 time to fit residues: 15.0923 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 40.0000 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 188 optimal weight: 0.0010 overall best weight: 4.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110665 restraints weight = 31703.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108162 restraints weight = 55989.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.109220 restraints weight = 54295.955| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10414 Z= 0.215 Angle : 0.568 8.263 14504 Z= 0.358 Chirality : 0.043 0.188 2031 Planarity : 0.003 0.017 2080 Dihedral : 5.266 31.180 2080 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.41 % Favored : 88.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 2059 helix: 1.38 (0.14), residues: 1346 sheet: -2.73 (0.43), residues: 108 loop : -3.81 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 1021) hydrogen bonds : angle 5.04705 ( 3015) covalent geometry : bond 0.00317 (10414) covalent geometry : angle 0.56774 (14504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.182 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0910 time to fit residues: 14.7693 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 207 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.131439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.111685 restraints weight = 31781.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108766 restraints weight = 43381.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.109358 restraints weight = 39915.996| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10414 Z= 0.174 Angle : 0.501 7.980 14504 Z= 0.312 Chirality : 0.042 0.172 2031 Planarity : 0.002 0.016 2080 Dihedral : 4.801 32.128 2080 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.05 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 2059 helix: 1.79 (0.14), residues: 1364 sheet: -2.64 (0.42), residues: 120 loop : -3.76 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 1021) hydrogen bonds : angle 4.44069 ( 3015) covalent geometry : bond 0.00262 (10414) covalent geometry : angle 0.50087 (14504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0960 time to fit residues: 15.4287 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 0.0030 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 148 optimal weight: 50.0000 chunk 18 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 46 optimal weight: 10.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.132371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.113101 restraints weight = 31399.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.112058 restraints weight = 49611.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.109491 restraints weight = 40349.563| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 10414 Z= 0.134 Angle : 0.437 6.871 14504 Z= 0.269 Chirality : 0.040 0.153 2031 Planarity : 0.002 0.014 2080 Dihedral : 4.290 31.208 2080 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.91 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 2059 helix: 2.24 (0.15), residues: 1370 sheet: -2.72 (0.42), residues: 118 loop : -3.67 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 1021) hydrogen bonds : angle 3.97538 ( 3015) covalent geometry : bond 0.00201 (10414) covalent geometry : angle 0.43745 (14504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0901 time to fit residues: 14.5288 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 190 optimal weight: 30.0000 chunk 175 optimal weight: 0.8980 chunk 178 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.129380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110548 restraints weight = 31652.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.108958 restraints weight = 53861.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108944 restraints weight = 48887.940| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 10414 Z= 0.254 Angle : 0.614 9.590 14504 Z= 0.390 Chirality : 0.045 0.227 2031 Planarity : 0.003 0.015 2080 Dihedral : 5.346 30.147 2080 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.21 % Favored : 86.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 2059 helix: 1.58 (0.14), residues: 1358 sheet: -3.06 (0.42), residues: 107 loop : -3.91 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.05714 ( 1021) hydrogen bonds : angle 4.99401 ( 3015) covalent geometry : bond 0.00382 (10414) covalent geometry : angle 0.61423 (14504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.362 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0956 time to fit residues: 15.6545 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 163 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.129839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.110780 restraints weight = 31804.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.109061 restraints weight = 56527.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109734 restraints weight = 51873.536| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10414 Z= 0.222 Angle : 0.569 9.394 14504 Z= 0.356 Chirality : 0.044 0.208 2031 Planarity : 0.003 0.015 2080 Dihedral : 5.119 32.488 2080 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.56 % Favored : 88.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.20), residues: 2059 helix: 1.60 (0.14), residues: 1363 sheet: -3.18 (0.41), residues: 114 loop : -3.93 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 1021) hydrogen bonds : angle 4.72779 ( 3015) covalent geometry : bond 0.00334 (10414) covalent geometry : angle 0.56880 (14504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0918 time to fit residues: 15.0190 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 20 optimal weight: 0.7980 chunk 58 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 192 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113343 restraints weight = 32060.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.111905 restraints weight = 50211.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111402 restraints weight = 41154.933| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10414 Z= 0.124 Angle : 0.425 6.599 14504 Z= 0.261 Chirality : 0.040 0.147 2031 Planarity : 0.002 0.013 2080 Dihedral : 4.299 30.126 2080 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.57 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 2059 helix: 2.31 (0.15), residues: 1368 sheet: -3.06 (0.40), residues: 120 loop : -3.69 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 1021) hydrogen bonds : angle 3.93184 ( 3015) covalent geometry : bond 0.00186 (10414) covalent geometry : angle 0.42547 (14504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.317 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1061 time to fit residues: 17.2254 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 205 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.134935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.116219 restraints weight = 31716.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115177 restraints weight = 49113.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114959 restraints weight = 42396.023| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.031 10414 Z= 0.074 Angle : 0.350 5.320 14504 Z= 0.212 Chirality : 0.038 0.138 2031 Planarity : 0.001 0.013 2080 Dihedral : 3.531 27.669 2080 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 2059 helix: 2.84 (0.15), residues: 1374 sheet: -2.65 (0.42), residues: 115 loop : -3.53 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.02534 ( 1021) hydrogen bonds : angle 3.31223 ( 3015) covalent geometry : bond 0.00108 (10414) covalent geometry : angle 0.35023 (14504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.864 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1057 time to fit residues: 16.8918 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 9 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 47 optimal weight: 0.0570 chunk 131 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.133133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.114637 restraints weight = 31756.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113076 restraints weight = 47283.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111070 restraints weight = 41485.562| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.041 10414 Z= 0.101 Angle : 0.380 5.739 14504 Z= 0.233 Chirality : 0.039 0.141 2031 Planarity : 0.002 0.012 2080 Dihedral : 3.732 27.297 2080 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.62 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.21), residues: 2059 helix: 2.84 (0.15), residues: 1379 sheet: -2.61 (0.43), residues: 118 loop : -3.52 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 1021) hydrogen bonds : angle 3.50233 ( 3015) covalent geometry : bond 0.00149 (10414) covalent geometry : angle 0.38049 (14504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0913 time to fit residues: 14.9061 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 32 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 76 optimal weight: 0.0060 chunk 200 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.130932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111221 restraints weight = 31908.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108097 restraints weight = 52519.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108900 restraints weight = 48335.576| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 10414 Z= 0.166 Angle : 0.475 7.269 14504 Z= 0.297 Chirality : 0.041 0.165 2031 Planarity : 0.002 0.013 2080 Dihedral : 4.392 27.138 2080 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.22 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 2059 helix: 2.52 (0.14), residues: 1370 sheet: -2.67 (0.45), residues: 112 loop : -3.68 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 1021) hydrogen bonds : angle 4.12220 ( 3015) covalent geometry : bond 0.00247 (10414) covalent geometry : angle 0.47527 (14504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4118 Ramachandran restraints generated. 2059 Oldfield, 0 Emsley, 2059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0900 time to fit residues: 14.6221 Evaluate side-chains 77 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 180 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 139 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.129535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109579 restraints weight = 31835.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106603 restraints weight = 55873.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107316 restraints weight = 49468.348| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10414 Z= 0.217 Angle : 0.556 8.872 14504 Z= 0.351 Chirality : 0.043 0.200 2031 Planarity : 0.003 0.014 2080 Dihedral : 4.983 28.776 2080 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.58 % Favored : 87.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 2059 helix: 2.01 (0.14), residues: 1366 sheet: -3.00 (0.43), residues: 114 loop : -3.78 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 23 PHE 0.000 0.000 PHE A 17 TYR 0.000 0.000 TYR A 30 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 1021) hydrogen bonds : angle 4.66438 ( 3015) covalent geometry : bond 0.00323 (10414) covalent geometry : angle 0.55648 (14504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.94 seconds wall clock time: 52 minutes 33.66 seconds (3153.66 seconds total)