Starting phenix.real_space_refine on Mon Sep 30 01:10:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b03_44026/09_2024/9b03_44026.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b03_44026/09_2024/9b03_44026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b03_44026/09_2024/9b03_44026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b03_44026/09_2024/9b03_44026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b03_44026/09_2024/9b03_44026.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b03_44026/09_2024/9b03_44026.cif" } resolution = 2.95 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= 0.008 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 154 5.16 5 C 15072 2.51 5 N 4074 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23896 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3171 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain breaks: 2 Chain: "H" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3157 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.68, per 1000 atoms: 0.57 Number of scatterers: 23896 At special positions: 0 Unit cell: (129.6, 132.84, 222.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 154 16.00 P 12 15.00 Mg 6 11.99 O 4578 8.00 N 4074 7.00 C 15072 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.06 Conformation dependent library (CDL) restraints added in 2.9 seconds 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 36 sheets defined 56.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.596A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.780A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.575A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.957A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 4.123A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.749A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.535A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.659A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.570A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.608A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.571A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.677A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.596A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.723A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.805A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.531A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.567A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.008A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.721A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.946A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.577A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.764A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.692A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.607A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.652A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.189A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.579A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.591A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.856A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.748A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 217 removed outlier: 4.133A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.648A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.527A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.188A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.613A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.738A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.850A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.529A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.707A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.953A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.607A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 263 through 268 removed outlier: 3.540A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.189A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.680A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.585A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.079A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.558A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.761A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.867A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.706A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.968A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.645A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.529A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.680A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.659A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.666A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.551A pdb=" N PHE E 352 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.926A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.630A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.695A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.162A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.823A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.577A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.803A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.859A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.569A pdb=" N ILE F 267 " --> pdb=" O PRO F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.638A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.085A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.601A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 349 through 356 removed outlier: 3.516A pdb=" N PHE F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.172A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 578 Processing helix chain 'G' and resid 582 through 589 removed outlier: 4.506A pdb=" N SER G 586 " --> pdb=" O SER G 582 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 587 " --> pdb=" O MET G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 606 Processing helix chain 'G' and resid 634 through 645 Processing helix chain 'G' and resid 651 through 661 Processing helix chain 'G' and resid 668 through 678 Processing helix chain 'G' and resid 681 through 691 Processing helix chain 'G' and resid 699 through 710 Processing helix chain 'G' and resid 713 through 750 removed outlier: 3.709A pdb=" N ARG G 717 " --> pdb=" O CYS G 713 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET G 733 " --> pdb=" O ALA G 729 " (cutoff:3.500A) Proline residue: G 736 - end of helix Processing helix chain 'G' and resid 752 through 769 removed outlier: 3.752A pdb=" N ILE G 756 " --> pdb=" O ARG G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 781 through 790 removed outlier: 3.960A pdb=" N THR G 784 " --> pdb=" O LYS G 781 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU G 785 " --> pdb=" O ILE G 782 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 786 " --> pdb=" O SER G 783 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 788 " --> pdb=" O LEU G 785 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR G 789 " --> pdb=" O LEU G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 799 through 811 removed outlier: 3.948A pdb=" N LYS G 810 " --> pdb=" O GLU G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 812 through 816 removed outlier: 3.584A pdb=" N LEU G 815 " --> pdb=" O HIS G 812 " (cutoff:3.500A) Processing helix chain 'G' and resid 817 through 822 removed outlier: 3.809A pdb=" N ASP G 821 " --> pdb=" O GLN G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 829 Processing helix chain 'G' and resid 832 through 856 removed outlier: 3.832A pdb=" N ILE G 836 " --> pdb=" O ASN G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 858 through 897 removed outlier: 3.800A pdb=" N GLN G 864 " --> pdb=" O GLU G 860 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU G 867 " --> pdb=" O GLU G 863 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG G 868 " --> pdb=" O GLN G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 905 through 947 removed outlier: 3.675A pdb=" N THR G 909 " --> pdb=" O SER G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 972 through 980 removed outlier: 3.706A pdb=" N ASP G 979 " --> pdb=" O ALA G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 981 through 983 No H-bonds generated for 'chain 'G' and resid 981 through 983' Processing helix chain 'H' and resid 573 through 578 Processing helix chain 'H' and resid 582 through 589 Processing helix chain 'H' and resid 598 through 606 removed outlier: 3.750A pdb=" N ILE H 602 " --> pdb=" O ASP H 598 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 647 removed outlier: 3.824A pdb=" N GLN H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 662 removed outlier: 3.510A pdb=" N VAL H 655 " --> pdb=" O SER H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 removed outlier: 3.617A pdb=" N LEU H 672 " --> pdb=" O ASP H 668 " (cutoff:3.500A) Processing helix chain 'H' and resid 681 through 690 Processing helix chain 'H' and resid 694 through 698 removed outlier: 3.594A pdb=" N LYS H 697 " --> pdb=" O GLU H 694 " (cutoff:3.500A) Processing helix chain 'H' and resid 699 through 710 Processing helix chain 'H' and resid 713 through 750 removed outlier: 3.863A pdb=" N ARG H 717 " --> pdb=" O CYS H 713 " (cutoff:3.500A) Proline residue: H 736 - end of helix Processing helix chain 'H' and resid 752 through 769 removed outlier: 3.895A pdb=" N ILE H 756 " --> pdb=" O ARG H 752 " (cutoff:3.500A) Processing helix chain 'H' and resid 781 through 788 removed outlier: 3.558A pdb=" N LEU H 785 " --> pdb=" O ILE H 782 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 786 " --> pdb=" O SER H 783 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 788 " --> pdb=" O LEU H 785 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 811 removed outlier: 3.622A pdb=" N LYS H 810 " --> pdb=" O GLU H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 816 Processing helix chain 'H' and resid 817 through 822 removed outlier: 3.570A pdb=" N ASP H 821 " --> pdb=" O GLN H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 822 through 828 Processing helix chain 'H' and resid 832 through 856 removed outlier: 3.837A pdb=" N ILE H 836 " --> pdb=" O ASN H 832 " (cutoff:3.500A) Processing helix chain 'H' and resid 858 through 897 removed outlier: 3.540A pdb=" N GLN H 862 " --> pdb=" O VAL H 858 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 864 " --> pdb=" O GLU H 860 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU H 867 " --> pdb=" O GLU H 863 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG H 868 " --> pdb=" O GLN H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 905 through 947 Processing helix chain 'H' and resid 972 through 979 removed outlier: 3.824A pdb=" N ASP H 979 " --> pdb=" O ALA H 975 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.358A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.240A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.924A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.337A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.636A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.945A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.327A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.223A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.781A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.823A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.623A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.740A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.813A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E 103 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.251A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.990A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR F 133 " --> pdb=" O THR F 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.921A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1224 hydrogen bonds defined for protein. 3330 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: 9.99 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6296 1.34 - 1.46: 4622 1.46 - 1.58: 13174 1.58 - 1.70: 18 1.70 - 1.82: 262 Bond restraints: 24372 Sorted by residual: bond pdb=" N GLU G 948 " pdb=" CA GLU G 948 " ideal model delta sigma weight residual 1.456 1.504 -0.047 1.23e-02 6.61e+03 1.49e+01 bond pdb=" C GLU G 947 " pdb=" N GLU G 948 " ideal model delta sigma weight residual 1.331 1.370 -0.039 1.35e-02 5.49e+03 8.37e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.02e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 ... (remaining 24367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 32168 2.63 - 5.26: 705 5.26 - 7.89: 107 7.89 - 10.52: 29 10.52 - 13.15: 4 Bond angle restraints: 33013 Sorted by residual: angle pdb=" N GLU B 364 " pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " ideal model delta sigma weight residual 110.20 118.62 -8.42 1.49e+00 4.50e-01 3.20e+01 angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" CB GLU A 364 " ideal model delta sigma weight residual 110.07 117.71 -7.64 1.45e+00 4.76e-01 2.77e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" CA MET F 47 " pdb=" CB MET F 47 " pdb=" CG MET F 47 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.44e+01 angle pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " pdb=" CG GLU B 364 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 ... (remaining 33008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 14140 24.07 - 48.15: 629 48.15 - 72.22: 53 72.22 - 96.30: 8 96.30 - 120.37: 3 Dihedral angle restraints: 14833 sinusoidal: 6047 harmonic: 8786 Sorted by residual: dihedral pdb=" CA GLU G 947 " pdb=" C GLU G 947 " pdb=" N GLU G 948 " pdb=" CA GLU G 948 " ideal model delta harmonic sigma weight residual -180.00 -139.87 -40.13 0 5.00e+00 4.00e-02 6.44e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.63 120.37 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 49.09 -109.09 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 14830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3254 0.088 - 0.176: 410 0.176 - 0.264: 29 0.264 - 0.352: 5 0.352 - 0.440: 2 Chirality restraints: 3700 Sorted by residual: chirality pdb=" CB ILE D 287 " pdb=" CA ILE D 287 " pdb=" CG1 ILE D 287 " pdb=" CG2 ILE D 287 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CB ILE G 980 " pdb=" CA ILE G 980 " pdb=" CG1 ILE G 980 " pdb=" CG2 ILE G 980 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 3697 not shown) Planarity restraints: 4237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 947 " -0.034 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" C GLU G 947 " 0.119 2.00e-02 2.50e+03 pdb=" O GLU G 947 " -0.046 2.00e-02 2.50e+03 pdb=" N GLU G 948 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 111 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 112 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 896 " -0.022 2.00e-02 2.50e+03 2.20e-02 9.67e+00 pdb=" CG TYR H 896 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR H 896 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 896 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR H 896 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR H 896 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 896 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 896 " 0.002 2.00e-02 2.50e+03 ... (remaining 4234 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 238 2.66 - 3.22: 19918 3.22 - 3.78: 36956 3.78 - 4.34: 52000 4.34 - 4.90: 84320 Nonbonded interactions: 193432 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.097 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.207 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.310 2.170 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.332 3.040 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.336 3.040 ... (remaining 193427 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 551 through 947 or resid 971 through 983)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 54.520 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.170 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.005 0.078 24372 Z= 0.331 Angle : 0.962 13.155 33013 Z= 0.508 Chirality : 0.056 0.440 3700 Planarity : 0.007 0.090 4237 Dihedral : 13.377 120.369 9161 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.06 (0.13), residues: 2978 helix: -1.72 (0.10), residues: 1484 sheet: -0.63 (0.24), residues: 396 loop : -0.77 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 569 HIS 0.011 0.001 HIS H 803 PHE 0.033 0.002 PHE F 223 TYR 0.053 0.002 TYR H 896 ARG 0.007 0.001 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8036 (tpp) cc_final: 0.7278 (tpt) REVERT: A 355 MET cc_start: 0.8059 (mmm) cc_final: 0.7233 (tpp) REVERT: C 227 MET cc_start: 0.8660 (mmm) cc_final: 0.8314 (mmm) REVERT: E 283 MET cc_start: 0.9125 (mmm) cc_final: 0.8878 (mmm) REVERT: G 721 MET cc_start: 0.9175 (mmp) cc_final: 0.8863 (mmm) REVERT: H 554 HIS cc_start: 0.3135 (p-80) cc_final: 0.2847 (p-80) REVERT: H 733 MET cc_start: 0.9271 (ptt) cc_final: 0.9042 (tmm) REVERT: H 974 ASP cc_start: 0.8582 (t0) cc_final: 0.8349 (m-30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 1.5068 time to fit residues: 279.8193 Evaluate side-chains 134 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN C 12 ASN C 161 HIS C 162 ASN E 40 HIS ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 647 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 24372 Z= 0.413 Angle : 0.706 9.806 33013 Z= 0.351 Chirality : 0.046 0.193 3700 Planarity : 0.005 0.065 4237 Dihedral : 7.235 132.972 3350 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.86 % Allowed : 5.25 % Favored : 93.89 % 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: -0.22 (0.15), residues: 2978 helix: 0.12 (0.13), residues: 1479 sheet: -0.27 (0.26), residues: 372 loop : -0.24 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 86 HIS 0.017 0.001 HIS H 812 PHE 0.033 0.002 PHE H 757 TYR 0.018 0.002 TYR A 294 ARG 0.007 0.001 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 2.703 Fit side-chains revert: symmetry clash REVERT: B 132 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7886 (tmt) REVERT: F 305 MET cc_start: 0.8295 (mmm) cc_final: 0.7962 (tpp) REVERT: F 375 PHE cc_start: 0.7562 (t80) cc_final: 0.7229 (t80) REVERT: G 554 HIS cc_start: 0.0435 (p90) cc_final: 0.0228 (p-80) REVERT: G 721 MET cc_start: 0.9173 (mmp) cc_final: 0.8406 (mmm) REVERT: H 554 HIS cc_start: 0.2950 (p-80) cc_final: 0.2656 (p-80) REVERT: H 733 MET cc_start: 0.9210 (ptt) cc_final: 0.8945 (tmm) REVERT: H 757 PHE cc_start: 0.8839 (m-10) cc_final: 0.8550 (m-80) REVERT: H 974 ASP cc_start: 0.8586 (t0) cc_final: 0.8231 (m-30) outliers start: 22 outliers final: 3 residues processed: 143 average time/residue: 1.4818 time to fit residues: 243.3523 Evaluate side-chains 132 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain G residue 724 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.1980 chunk 226 optimal weight: 0.6980 chunk 185 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 243 optimal weight: 30.0000 chunk 270 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 218 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24372 Z= 0.175 Angle : 0.575 8.497 33013 Z= 0.274 Chirality : 0.042 0.167 3700 Planarity : 0.004 0.055 4237 Dihedral : 6.865 125.573 3350 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.78 % Allowed : 6.30 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.16), residues: 2978 helix: 0.85 (0.14), residues: 1473 sheet: -0.36 (0.25), residues: 402 loop : 0.09 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS D 371 PHE 0.021 0.001 PHE D 375 TYR 0.011 0.001 TYR G 865 ARG 0.004 0.000 ARG H 940 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9068 (mtt) cc_final: 0.8844 (mtt) REVERT: C 44 MET cc_start: 0.6807 (mtp) cc_final: 0.6431 (mtm) REVERT: C 82 MET cc_start: 0.7853 (tpt) cc_final: 0.7630 (tpt) REVERT: C 132 MET cc_start: 0.8444 (ppp) cc_final: 0.8100 (ttt) REVERT: C 227 MET cc_start: 0.8686 (mmm) cc_final: 0.8226 (mmm) REVERT: D 123 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7186 (tmt) REVERT: E 47 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4806 (pmm) REVERT: F 313 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7766 (mmt) REVERT: F 375 PHE cc_start: 0.7451 (t80) cc_final: 0.7181 (t80) REVERT: G 721 MET cc_start: 0.9172 (mmp) cc_final: 0.8661 (mmm) REVERT: G 865 TYR cc_start: 0.6525 (m-10) cc_final: 0.6113 (m-10) REVERT: H 554 HIS cc_start: 0.2913 (p-80) cc_final: 0.2623 (p-80) REVERT: H 733 MET cc_start: 0.9228 (ptt) cc_final: 0.8967 (tmm) REVERT: H 974 ASP cc_start: 0.8592 (t0) cc_final: 0.8243 (m-30) outliers start: 20 outliers final: 6 residues processed: 141 average time/residue: 1.4751 time to fit residues: 238.5761 Evaluate side-chains 137 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain F residue 313 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 130 optimal weight: 0.0060 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 7.9990 chunk 289 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 ASN D 173 HIS F 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24372 Z= 0.131 Angle : 0.546 8.622 33013 Z= 0.257 Chirality : 0.041 0.162 3700 Planarity : 0.003 0.050 4237 Dihedral : 6.420 110.206 3350 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.97 % Allowed : 7.35 % Favored : 91.68 % 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: 1.00 (0.16), residues: 2978 helix: 1.33 (0.14), residues: 1465 sheet: -0.18 (0.25), residues: 402 loop : 0.27 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 584 HIS 0.009 0.001 HIS H 812 PHE 0.021 0.001 PHE D 375 TYR 0.020 0.001 TYR H 714 ARG 0.004 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8390 (tpt) cc_final: 0.8057 (tpt) REVERT: A 119 MET cc_start: 0.8563 (ptt) cc_final: 0.8322 (ptp) REVERT: B 123 MET cc_start: 0.8027 (tpp) cc_final: 0.7329 (tpp) REVERT: C 132 MET cc_start: 0.8378 (ppp) cc_final: 0.8006 (ttt) REVERT: C 227 MET cc_start: 0.8704 (mmm) cc_final: 0.8245 (mmm) REVERT: E 44 MET cc_start: 0.8707 (mtm) cc_final: 0.8256 (mmm) REVERT: E 47 MET cc_start: 0.4872 (pmm) cc_final: 0.4204 (pmm) REVERT: E 305 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7640 (mpp) REVERT: F 25 ASP cc_start: 0.7986 (t0) cc_final: 0.7557 (t0) REVERT: F 44 MET cc_start: 0.7469 (mmm) cc_final: 0.7171 (ttt) REVERT: F 375 PHE cc_start: 0.7357 (t80) cc_final: 0.7078 (t80) REVERT: G 721 MET cc_start: 0.9165 (mmp) cc_final: 0.8746 (mmm) REVERT: H 554 HIS cc_start: 0.2821 (p-80) cc_final: 0.2520 (p-80) REVERT: H 733 MET cc_start: 0.9235 (ptt) cc_final: 0.8999 (tmm) REVERT: H 974 ASP cc_start: 0.8557 (t0) cc_final: 0.8210 (m-30) outliers start: 25 outliers final: 3 residues processed: 142 average time/residue: 1.4929 time to fit residues: 244.2426 Evaluate side-chains 135 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 683 HIS ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24372 Z= 0.205 Angle : 0.574 8.942 33013 Z= 0.271 Chirality : 0.042 0.161 3700 Planarity : 0.003 0.044 4237 Dihedral : 6.411 112.976 3350 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.01 % Allowed : 8.09 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.16), residues: 2978 helix: 1.54 (0.14), residues: 1466 sheet: -0.20 (0.25), residues: 402 loop : 0.29 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 584 HIS 0.004 0.001 HIS H 812 PHE 0.023 0.001 PHE D 375 TYR 0.014 0.001 TYR H 896 ARG 0.003 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8546 (ptt) cc_final: 0.8299 (ptp) REVERT: C 227 MET cc_start: 0.8651 (mmm) cc_final: 0.8211 (mmm) REVERT: F 25 ASP cc_start: 0.7980 (t0) cc_final: 0.7575 (t0) REVERT: F 132 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7440 (ppp) REVERT: F 305 MET cc_start: 0.8313 (mmm) cc_final: 0.7277 (mpp) REVERT: F 375 PHE cc_start: 0.7459 (t80) cc_final: 0.7206 (t80) REVERT: G 721 MET cc_start: 0.9159 (mmp) cc_final: 0.8755 (mmm) REVERT: H 554 HIS cc_start: 0.2903 (p-80) cc_final: 0.2579 (p-80) REVERT: H 733 MET cc_start: 0.9191 (ptt) cc_final: 0.8969 (tmm) REVERT: H 974 ASP cc_start: 0.8601 (t0) cc_final: 0.8255 (m-30) outliers start: 26 outliers final: 10 residues processed: 140 average time/residue: 1.4992 time to fit residues: 240.3721 Evaluate side-chains 137 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain G residue 733 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 240 optimal weight: 5.9990 chunk 134 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 ASN ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24372 Z= 0.286 Angle : 0.614 8.941 33013 Z= 0.293 Chirality : 0.043 0.164 3700 Planarity : 0.003 0.039 4237 Dihedral : 6.619 121.920 3350 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.89 % Allowed : 9.30 % Favored : 89.81 % 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: 1.11 (0.16), residues: 2978 helix: 1.51 (0.14), residues: 1465 sheet: -0.29 (0.25), residues: 402 loop : 0.24 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.004 0.001 HIS D 87 PHE 0.025 0.001 PHE D 375 TYR 0.011 0.001 TYR H 714 ARG 0.004 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8227 (tpt) cc_final: 0.7920 (tpt) REVERT: B 123 MET cc_start: 0.8036 (tpp) cc_final: 0.7763 (tpt) REVERT: B 355 MET cc_start: 0.7678 (mtp) cc_final: 0.7366 (ttm) REVERT: C 227 MET cc_start: 0.8518 (mmm) cc_final: 0.8157 (mmm) REVERT: E 47 MET cc_start: 0.5626 (pmm) cc_final: 0.5373 (pmm) REVERT: E 132 MET cc_start: 0.7464 (pp-130) cc_final: 0.7170 (pp-130) REVERT: F 305 MET cc_start: 0.8473 (mmm) cc_final: 0.8029 (tpp) REVERT: F 375 PHE cc_start: 0.7465 (t80) cc_final: 0.7199 (t80) REVERT: G 721 MET cc_start: 0.9138 (mmp) cc_final: 0.8565 (mmm) REVERT: G 865 TYR cc_start: 0.6568 (m-10) cc_final: 0.5988 (m-10) REVERT: H 554 HIS cc_start: 0.2960 (p-80) cc_final: 0.2654 (p-80) REVERT: H 733 MET cc_start: 0.9195 (ptt) cc_final: 0.8939 (tmm) REVERT: H 757 PHE cc_start: 0.8829 (m-10) cc_final: 0.8539 (m-80) REVERT: H 974 ASP cc_start: 0.8621 (t0) cc_final: 0.8261 (m-30) outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 1.4280 time to fit residues: 241.1019 Evaluate side-chains 140 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 2.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain G residue 835 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 0.0670 chunk 164 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 289 optimal weight: 20.0000 chunk 180 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 ASN H 812 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24372 Z= 0.145 Angle : 0.562 10.872 33013 Z= 0.261 Chirality : 0.041 0.164 3700 Planarity : 0.003 0.040 4237 Dihedral : 6.349 110.087 3350 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.66 % Allowed : 9.61 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 2978 helix: 1.75 (0.14), residues: 1460 sheet: -0.16 (0.25), residues: 402 loop : 0.37 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 79 HIS 0.003 0.001 HIS D 371 PHE 0.021 0.001 PHE D 375 TYR 0.022 0.001 TYR H 865 ARG 0.005 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8336 (tpt) cc_final: 0.8091 (tpt) REVERT: A 119 MET cc_start: 0.8533 (ptt) cc_final: 0.8290 (ptp) REVERT: B 355 MET cc_start: 0.7615 (mtp) cc_final: 0.7281 (ttm) REVERT: C 227 MET cc_start: 0.8474 (mmm) cc_final: 0.8176 (mmm) REVERT: E 47 MET cc_start: 0.5690 (pmm) cc_final: 0.5357 (pmm) REVERT: E 132 MET cc_start: 0.7436 (pp-130) cc_final: 0.7200 (pp-130) REVERT: F 25 ASP cc_start: 0.7918 (t0) cc_final: 0.7539 (t0) REVERT: F 305 MET cc_start: 0.8477 (mmm) cc_final: 0.8043 (tpp) REVERT: F 375 PHE cc_start: 0.7461 (t80) cc_final: 0.7173 (t80) REVERT: G 721 MET cc_start: 0.9128 (mmp) cc_final: 0.8859 (mmm) REVERT: G 865 TYR cc_start: 0.6619 (m-10) cc_final: 0.6304 (m-10) REVERT: H 554 HIS cc_start: 0.2998 (p-80) cc_final: 0.2672 (p-80) REVERT: H 682 LYS cc_start: 0.9007 (mppt) cc_final: 0.8267 (tppt) REVERT: H 733 MET cc_start: 0.9199 (ptt) cc_final: 0.8933 (tmm) REVERT: H 757 PHE cc_start: 0.8839 (m-10) cc_final: 0.8566 (m-80) REVERT: H 974 ASP cc_start: 0.8548 (t0) cc_final: 0.8189 (m-30) outliers start: 17 outliers final: 9 residues processed: 136 average time/residue: 1.5449 time to fit residues: 240.1002 Evaluate side-chains 134 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 339 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.303 > 50: distance: 73 - 161: 13.561 distance: 76 - 158: 13.736 distance: 84 - 146: 20.822 distance: 87 - 143: 22.650 distance: 110 - 115: 4.882 distance: 115 - 116: 3.581 distance: 116 - 117: 8.710 distance: 116 - 119: 3.768 distance: 117 - 118: 8.180 distance: 117 - 123: 10.329 distance: 119 - 120: 3.658 distance: 120 - 121: 5.950 distance: 120 - 122: 3.678 distance: 124 - 125: 9.586 distance: 125 - 126: 7.927 distance: 125 - 127: 9.070 distance: 127 - 128: 26.586 distance: 128 - 129: 15.633 distance: 128 - 131: 23.985 distance: 129 - 130: 22.294 distance: 129 - 136: 16.128 distance: 131 - 132: 16.407 distance: 132 - 133: 19.130 distance: 133 - 135: 12.547 distance: 136 - 137: 19.014 distance: 137 - 140: 23.176 distance: 138 - 143: 9.235 distance: 140 - 141: 10.558 distance: 140 - 142: 11.780 distance: 143 - 144: 6.724 distance: 144 - 145: 8.513 distance: 144 - 147: 9.272 distance: 145 - 146: 9.017 distance: 147 - 148: 5.659 distance: 147 - 149: 7.398 distance: 148 - 150: 11.499 distance: 151 - 152: 7.376 distance: 152 - 153: 3.685 distance: 152 - 155: 9.118 distance: 153 - 154: 6.526 distance: 153 - 158: 6.780 distance: 155 - 156: 6.130 distance: 155 - 157: 11.218 distance: 158 - 159: 4.564 distance: 159 - 160: 9.069 distance: 159 - 162: 9.591 distance: 160 - 161: 7.858 distance: 160 - 166: 9.346 distance: 162 - 163: 10.342 distance: 162 - 164: 16.591 distance: 163 - 165: 7.032 distance: 166 - 167: 9.176 distance: 167 - 168: 5.669 distance: 168 - 169: 8.569 distance: 168 - 170: 11.627 distance: 170 - 171: 3.160 distance: 171 - 172: 12.129 distance: 171 - 174: 10.730 distance: 172 - 173: 13.040 distance: 172 - 178: 5.552 distance: 173 - 205: 21.760 distance: 174 - 175: 7.891 distance: 175 - 176: 6.586 distance: 175 - 177: 5.300 distance: 178 - 179: 6.762 distance: 179 - 180: 6.394 distance: 179 - 182: 8.197 distance: 180 - 181: 11.445 distance: 180 - 187: 6.865 distance: 182 - 183: 4.860 distance: 183 - 184: 8.182 distance: 184 - 186: 3.410