Starting phenix.real_space_refine on Fri Mar 15 03:18:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxr_27774/03_2024/8dxr_27774.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxr_27774/03_2024/8dxr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxr_27774/03_2024/8dxr_27774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxr_27774/03_2024/8dxr_27774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxr_27774/03_2024/8dxr_27774.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dxr_27774/03_2024/8dxr_27774.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.55, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 4.80 Conformation dependent library (CDL) restraints added in 2.7 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: 1.02 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: 3.10 Time building geometry restraints manager: 5.02 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: 91.80 - 98.98: 1 98.98 - 106.15: 66 106.15 - 113.33: 5963 113.33 - 120.51: 4416 120.51 - 127.69: 4058 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 2.520 nonbonded pdb=" O TYR C 123 " pdb=" N TYR C 126 " model vdw 2.355 2.520 nonbonded pdb=" O LEU C 283 " pdb=" N LYS C 286 " model vdw 2.386 2.520 nonbonded pdb=" O GLU A 234 " pdb=" N ALA A 238 " model vdw 2.389 2.520 nonbonded pdb=" O VAL D 252 " pdb=" N GLU D 254 " model vdw 2.389 2.520 ... (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 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.050 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 32.300 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.280 ------------------------------------------------------------------------------- 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= 0.267 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0894 time to fit residues: 14.5651 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 188 optimal weight: 0.7980 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 10414 Z= 0.327 Angle : 0.698 9.756 14504 Z= 0.446 Chirality : 0.047 0.230 2031 Planarity : 0.004 0.021 2080 Dihedral : 6.035 31.056 2080 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.08 % Favored : 85.77 % 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 (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: -1.19 (0.19), residues: 2059 helix: 0.72 (0.14), residues: 1345 sheet: -2.80 (0.44), residues: 107 loop : -3.99 (0.23), residues: 607 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.152 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0912 time to fit residues: 14.7691 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 chunk 128 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10414 Z= 0.241 Angle : 0.565 9.204 14504 Z= 0.354 Chirality : 0.043 0.203 2031 Planarity : 0.003 0.020 2080 Dihedral : 5.300 32.240 2080 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.07 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: -0.54 (0.19), residues: 2059 helix: 1.34 (0.14), residues: 1345 sheet: -2.92 (0.40), residues: 117 loop : -3.97 (0.23), residues: 597 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0886 time to fit residues: 14.4828 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.0870 chunk 142 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 90 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 189 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 179 optimal weight: 0.0980 chunk 54 optimal weight: 20.0000 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 10414 Z= 0.076 Angle : 0.358 5.996 14504 Z= 0.219 Chirality : 0.038 0.138 2031 Planarity : 0.001 0.014 2080 Dihedral : 3.715 31.516 2080 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.20 % 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: 0.98 (0.21), residues: 2059 helix: 2.52 (0.15), residues: 1366 sheet: -2.38 (0.44), residues: 111 loop : -3.62 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0910 time to fit residues: 14.6971 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10414 Z= 0.134 Angle : 0.414 6.230 14504 Z= 0.256 Chirality : 0.040 0.140 2031 Planarity : 0.002 0.014 2080 Dihedral : 4.056 29.125 2080 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.39 % Favored : 89.51 % 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: 0.90 (0.21), residues: 2059 helix: 2.48 (0.15), residues: 1371 sheet: -2.63 (0.42), residues: 118 loop : -3.72 (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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.149 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0884 time to fit residues: 14.4690 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 93 optimal weight: 0.0670 chunk 16 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.030 10414 Z= 0.084 Angle : 0.354 5.489 14504 Z= 0.215 Chirality : 0.038 0.141 2031 Planarity : 0.001 0.013 2080 Dihedral : 3.524 27.371 2080 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 0.67 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: 1.32 (0.21), residues: 2059 helix: 2.77 (0.15), residues: 1373 sheet: -2.26 (0.45), residues: 115 loop : -3.56 (0.24), 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.300 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0877 time to fit residues: 14.3578 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 0.0670 chunk 112 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10414 Z= 0.142 Angle : 0.417 6.185 14504 Z= 0.258 Chirality : 0.040 0.142 2031 Planarity : 0.002 0.013 2080 Dihedral : 3.970 27.088 2080 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.10 % 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 : 0.00 % 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: 1.13 (0.21), residues: 2059 helix: 2.65 (0.15), residues: 1374 sheet: -2.53 (0.44), residues: 113 loop : -3.63 (0.24), residues: 572 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0915 time to fit residues: 14.8696 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 0.0770 chunk 127 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 overall best weight: 1.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.040 10414 Z= 0.107 Angle : 0.376 5.340 14504 Z= 0.229 Chirality : 0.039 0.140 2031 Planarity : 0.002 0.012 2080 Dihedral : 3.672 27.039 2080 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.33 % Favored : 92.57 % 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: 1.38 (0.21), residues: 2059 helix: 2.83 (0.15), residues: 1373 sheet: -2.55 (0.43), residues: 120 loop : -3.48 (0.24), residues: 566 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0943 time to fit residues: 15.2466 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 186 optimal weight: 0.0060 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 176 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.038 10414 Z= 0.097 Angle : 0.359 5.204 14504 Z= 0.219 Chirality : 0.038 0.141 2031 Planarity : 0.001 0.012 2080 Dihedral : 3.474 26.305 2080 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.60 % Favored : 91.31 % 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: 1.60 (0.21), residues: 2059 helix: 3.01 (0.14), residues: 1377 sheet: -2.34 (0.45), residues: 116 loop : -3.50 (0.24), residues: 566 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0912 time to fit residues: 14.6891 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 chunk 165 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 131 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 10414 Z= 0.178 Angle : 0.462 7.057 14504 Z= 0.288 Chirality : 0.041 0.165 2031 Planarity : 0.002 0.012 2080 Dihedral : 4.245 25.759 2080 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.61 % 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 : 0.00 % 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: 1.16 (0.20), residues: 2059 helix: 2.66 (0.14), residues: 1370 sheet: -2.51 (0.45), residues: 112 loop : -3.56 (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 ********************** 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 fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0833 time to fit residues: 13.7836 Evaluate side-chains 77 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 145 optimal weight: 50.0000 overall best weight: 1.7622 ------------------------------------------------------------------------------- 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 = 0.133173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113976 restraints weight = 31435.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.114252 restraints weight = 49782.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.114070 restraints weight = 34299.070| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10414 Z= 0.116 Angle : 0.385 5.597 14504 Z= 0.236 Chirality : 0.039 0.135 2031 Planarity : 0.002 0.012 2080 Dihedral : 3.771 26.881 2080 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.21 % Favored : 91.69 % 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: 1.47 (0.21), residues: 2059 helix: 2.92 (0.14), residues: 1375 sheet: -2.51 (0.45), residues: 117 loop : -3.52 (0.24), residues: 567 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1566.63 seconds wall clock time: 28 minutes 34.05 seconds (1714.05 seconds total)