Starting phenix.real_space_refine on Sat Aug 23 06:44:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dxr_27774/08_2025/8dxr_27774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dxr_27774/08_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_27774/08_2025/8dxr_27774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dxr_27774/08_2025/8dxr_27774.map" model { file = "/net/cci-nas-00/data/ceres_data/8dxr_27774/08_2025/8dxr_27774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dxr_27774/08_2025/8dxr_27774.cif" } resolution = 4.0 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= 0.020 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 16, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 7} 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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 17, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 7} 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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 17, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 7} 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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 16, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 14, 'ASN:plan1': 9, 'HIS:plan': 7} 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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 17, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 13, 'ASN:plan1': 9, 'HIS:plan': 7} 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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 17, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 14, 'ASN:plan1': 9, 'HIS:plan': 7} 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: {'PHE:plan': 25, 'ARG:plan': 10, 'TRP:plan': 6, 'ASP:plan': 16, 'TYR:plan': 19, 'GLN:plan1': 12, 'GLU:plan': 14, 'ASN:plan1': 9, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 601 Time building chain proxies: 3.42, per 1000 atoms: 0.33 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: 1.24 Conformation dependent library (CDL) restraints added in 742.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 1.73 Time building geometry restraints manager: 1.56 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: 3.050 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.930 Find NCS groups from input model: 0.290 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.880 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00363 (10414) covalent geometry : angle 0.80720 (14504) hydrogen bonds : bond 0.15218 ( 1021) hydrogen bonds : angle 6.40054 ( 3015) *********************** 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 : 0.402 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0460 time to fit residues: 7.0532 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.9482 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.135407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116198 restraints weight = 31437.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114697 restraints weight = 49635.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.115211 restraints weight = 45486.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.114804 restraints weight = 30334.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.115047 restraints weight = 28518.996| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.025 10414 Z= 0.091 Angle : 0.393 5.683 14504 Z= 0.241 Chirality : 0.038 0.141 2031 Planarity : 0.002 0.017 2080 Dihedral : 4.068 30.928 2080 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.75 % Favored : 93.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.21), residues: 2059 helix: 2.35 (0.15), residues: 1356 sheet: -2.28 (0.44), residues: 121 loop : -3.51 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00127 (10414) covalent geometry : angle 0.39338 (14504) hydrogen bonds : bond 0.03257 ( 1021) hydrogen bonds : angle 3.91925 ( 3015) *********************** 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 : 0.420 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0468 time to fit residues: 7.3534 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 45 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.129305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111203 restraints weight = 31892.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.110790 restraints weight = 60147.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.110586 restraints weight = 41803.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.110282 restraints weight = 31955.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110432 restraints weight = 30864.984| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10414 Z= 0.235 Angle : 0.585 8.446 14504 Z= 0.372 Chirality : 0.044 0.203 2031 Planarity : 0.003 0.016 2080 Dihedral : 5.192 30.050 2080 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.95 % Favored : 87.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.20), residues: 2059 helix: 1.70 (0.14), residues: 1353 sheet: -2.57 (0.44), residues: 113 loop : -3.81 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00348 (10414) covalent geometry : angle 0.58481 (14504) hydrogen bonds : bond 0.05639 ( 1021) hydrogen bonds : angle 4.96075 ( 3015) *********************** 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 : 0.426 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0477 time to fit residues: 7.5104 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 10 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 71 optimal weight: 0.0870 chunk 61 optimal weight: 5.9990 chunk 177 optimal weight: 30.0000 chunk 97 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 133 optimal weight: 40.0000 chunk 41 optimal weight: 0.0060 chunk 139 optimal weight: 9.9990 overall best weight: 2.7578 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.132101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113244 restraints weight = 31760.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111799 restraints weight = 52350.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111567 restraints weight = 46594.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110869 restraints weight = 33496.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111248 restraints weight = 30544.745| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1490 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= 0.150 Angle : 0.465 7.699 14504 Z= 0.287 Chirality : 0.041 0.167 2031 Planarity : 0.002 0.014 2080 Dihedral : 4.520 31.146 2080 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.18 % Favored : 90.68 % 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 : 0.05 % 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 aren not related in a simple way. whole: 0.49 (0.20), residues: 2059 helix: 2.12 (0.15), residues: 1360 sheet: -2.55 (0.43), residues: 120 loop : -3.70 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00226 (10414) covalent geometry : angle 0.46460 (14504) hydrogen bonds : bond 0.04176 ( 1021) hydrogen bonds : angle 4.20622 ( 3015) *********************** 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 : 0.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0471 time to fit residues: 7.4503 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 : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.130359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110260 restraints weight = 31906.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107511 restraints weight = 58968.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.108383 restraints weight = 50741.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108797 restraints weight = 32944.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108989 restraints weight = 30985.517| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 10414 Z= 0.203 Angle : 0.538 8.433 14504 Z= 0.339 Chirality : 0.043 0.194 2031 Planarity : 0.003 0.014 2080 Dihedral : 5.027 30.331 2080 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.34 % Favored : 87.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.20), residues: 2059 helix: 1.80 (0.14), residues: 1362 sheet: -2.80 (0.43), residues: 108 loop : -3.81 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00301 (10414) covalent geometry : angle 0.53822 (14504) hydrogen bonds : bond 0.05161 ( 1021) hydrogen bonds : angle 4.67938 ( 3015) *********************** 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 : 0.417 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0442 time to fit residues: 6.9409 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 : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 163 optimal weight: 20.0000 chunk 100 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 178 optimal weight: 40.0000 chunk 135 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.130815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.110615 restraints weight = 32162.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107921 restraints weight = 55393.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108811 restraints weight = 50260.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109202 restraints weight = 31531.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.109404 restraints weight = 28909.264| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10414 Z= 0.191 Angle : 0.518 8.351 14504 Z= 0.323 Chirality : 0.042 0.180 2031 Planarity : 0.003 0.014 2080 Dihedral : 4.814 30.769 2080 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.44 % Favored : 89.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.20), residues: 2059 helix: 1.88 (0.14), residues: 1363 sheet: -2.92 (0.41), residues: 120 loop : -3.82 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00285 (10414) covalent geometry : angle 0.51784 (14504) hydrogen bonds : bond 0.04687 ( 1021) hydrogen bonds : angle 4.46019 ( 3015) *********************** 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 : 0.430 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0475 time to fit residues: 7.4249 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 : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 207 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 204 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 84 optimal weight: 0.0570 chunk 163 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 overall best weight: 3.5304 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.130393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111038 restraints weight = 31725.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110122 restraints weight = 54980.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108502 restraints weight = 43705.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107529 restraints weight = 44613.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.107837 restraints weight = 39235.607| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 10414 Z= 0.185 Angle : 0.514 8.487 14504 Z= 0.320 Chirality : 0.042 0.186 2031 Planarity : 0.002 0.014 2080 Dihedral : 4.852 29.677 2080 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.19 % Favored : 87.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 2059 helix: 1.93 (0.14), residues: 1364 sheet: -2.94 (0.42), residues: 113 loop : -3.83 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00277 (10414) covalent geometry : angle 0.51370 (14504) hydrogen bonds : bond 0.04765 ( 1021) hydrogen bonds : angle 4.45905 ( 3015) *********************** 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 : 0.648 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0466 time to fit residues: 7.5193 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 : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 184 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 70 optimal weight: 40.0000 chunk 120 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.125924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107893 restraints weight = 31945.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108239 restraints weight = 64293.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107464 restraints weight = 37192.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107279 restraints weight = 33767.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107318 restraints weight = 30363.624| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 10414 Z= 0.355 Angle : 0.768 11.394 14504 Z= 0.493 Chirality : 0.050 0.272 2031 Planarity : 0.004 0.020 2080 Dihedral : 6.186 31.628 2080 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.67 % Favored : 85.14 % 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 : 0.15 % 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 aren not related in a simple way. whole: -1.15 (0.19), residues: 2059 helix: 0.81 (0.14), residues: 1356 sheet: -3.32 (0.43), residues: 107 loop : -4.09 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00527 (10414) covalent geometry : angle 0.76775 (14504) hydrogen bonds : bond 0.06990 ( 1021) hydrogen bonds : angle 5.84614 ( 3015) *********************** 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 : 0.409 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0451 time to fit residues: 7.1296 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 : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 7.9990 chunk 143 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 154 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.127960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.109247 restraints weight = 32352.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107565 restraints weight = 55423.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106710 restraints weight = 44606.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105689 restraints weight = 38945.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106105 restraints weight = 35481.537| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 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 : 0.004 0.109 10414 Z= 0.277 Angle : 0.657 11.027 14504 Z= 0.415 Chirality : 0.046 0.249 2031 Planarity : 0.004 0.016 2080 Dihedral : 5.741 31.943 2080 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.65 % Favored : 86.16 % 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 : 0.10 % 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 aren not related in a simple way. whole: -0.92 (0.19), residues: 2059 helix: 0.98 (0.14), residues: 1361 sheet: -3.35 (0.43), residues: 112 loop : -4.00 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00417 (10414) covalent geometry : angle 0.65659 (14504) hydrogen bonds : bond 0.05891 ( 1021) hydrogen bonds : angle 5.26966 ( 3015) *********************** 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 : 0.420 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0460 time to fit residues: 7.1708 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 : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 0.0040 chunk 83 optimal weight: 0.3980 chunk 163 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 29 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 overall best weight: 4.8800 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.128401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.109479 restraints weight = 32009.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109089 restraints weight = 50585.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109162 restraints weight = 48865.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.108721 restraints weight = 34278.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.108962 restraints weight = 31379.305| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10414 Z= 0.247 Angle : 0.611 10.491 14504 Z= 0.384 Chirality : 0.045 0.230 2031 Planarity : 0.003 0.015 2080 Dihedral : 5.564 29.756 2080 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.31 % Favored : 86.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.19), residues: 2059 helix: 1.20 (0.14), residues: 1366 sheet: -3.39 (0.43), residues: 112 loop : -4.00 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00372 (10414) covalent geometry : angle 0.61089 (14504) hydrogen bonds : bond 0.05614 ( 1021) hydrogen bonds : angle 5.07806 ( 3015) ********************** 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 : 0.424 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0464 time to fit residues: 7.3240 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 : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 135 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.125762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106244 restraints weight = 32431.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.104341 restraints weight = 61204.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104970 restraints weight = 52786.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104952 restraints weight = 32644.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105183 restraints weight = 33413.366| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 10414 Z= 0.382 Angle : 0.816 12.696 14504 Z= 0.525 Chirality : 0.051 0.298 2031 Planarity : 0.005 0.021 2080 Dihedral : 6.576 33.020 2080 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.74 % Favored : 84.07 % 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 : 0.20 % 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 aren not related in a simple way. whole: -1.64 (0.18), residues: 2059 helix: 0.35 (0.14), residues: 1366 sheet: -3.35 (0.45), residues: 106 loop : -4.17 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 30 PHE 0.000 0.000 PHE A 17 TRP 0.000 0.000 TRP A 23 Details of bonding type rmsd covalent geometry : bond 0.00571 (10414) covalent geometry : angle 0.81595 (14504) hydrogen bonds : bond 0.07281 ( 1021) hydrogen bonds : angle 6.12632 ( 3015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1449.46 seconds wall clock time: 25 minutes 33.06 seconds (1533.06 seconds total)