Starting phenix.real_space_refine on Sat Jan 25 22:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b03_44026/01_2025/9b03_44026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b03_44026/01_2025/9b03_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/cci-nas-00/data/ceres_data/9b03_44026/01_2025/9b03_44026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b03_44026/01_2025/9b03_44026.map" model { file = "/net/cci-nas-00/data/ceres_data/9b03_44026/01_2025/9b03_44026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b03_44026/01_2025/9b03_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 13.24, per 1000 atoms: 0.55 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: 6.31 Conformation dependent library (CDL) restraints added in 3.2 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: 3.05 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: 9.39 Time building geometry restraints manager: 7.05 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: 1.460 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: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 52.660 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.460 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 2.851 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: 1.6281 time to fit residues: 301.8036 Evaluate side-chains 134 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 2.802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.079531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.058713 restraints weight = 99535.000| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.13 r_work: 0.3206 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 2.539 Fit side-chains revert: symmetry clash REVERT: B 132 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7839 (tmt) REVERT: F 305 MET cc_start: 0.8184 (mmm) cc_final: 0.7847 (tpp) REVERT: F 375 PHE cc_start: 0.7673 (t80) cc_final: 0.7280 (t80) REVERT: G 554 HIS cc_start: 0.0446 (p90) cc_final: 0.0130 (p-80) REVERT: G 721 MET cc_start: 0.9182 (mmp) cc_final: 0.8580 (mmm) REVERT: H 554 HIS cc_start: 0.2388 (p-80) cc_final: 0.2099 (p-80) REVERT: H 757 PHE cc_start: 0.8896 (m-10) cc_final: 0.8591 (m-80) REVERT: H 974 ASP cc_start: 0.8787 (t0) cc_final: 0.8352 (m-30) outliers start: 22 outliers final: 3 residues processed: 143 average time/residue: 1.6216 time to fit residues: 264.9958 Evaluate side-chains 132 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 3.267 ------------------------------------------------------------------------------- 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 160 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 157 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 278 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.080713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.058569 restraints weight = 98516.078| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.39 r_work: 0.3246 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24372 Z= 0.173 Angle : 0.576 9.481 33013 Z= 0.274 Chirality : 0.042 0.170 3700 Planarity : 0.004 0.054 4237 Dihedral : 6.850 125.139 3350 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.82 % Allowed : 6.34 % Favored : 92.84 % 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: 0.51 (0.16), residues: 2978 helix: 0.86 (0.14), residues: 1473 sheet: -0.35 (0.25), residues: 402 loop : 0.10 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 584 HIS 0.004 0.001 HIS D 371 PHE 0.021 0.001 PHE D 375 TYR 0.013 0.001 TYR G 865 ARG 0.005 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 156 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8459 (tpt) cc_final: 0.8259 (tpt) REVERT: B 132 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8076 (tmt) REVERT: C 44 MET cc_start: 0.6781 (mtp) cc_final: 0.6375 (mtm) REVERT: C 132 MET cc_start: 0.8179 (ppp) cc_final: 0.7638 (ttt) REVERT: C 227 MET cc_start: 0.8649 (mmm) cc_final: 0.8152 (mmm) REVERT: E 47 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5256 (pmm) REVERT: F 313 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7907 (mmt) REVERT: F 375 PHE cc_start: 0.7530 (t80) cc_final: 0.7206 (t80) REVERT: G 554 HIS cc_start: 0.0456 (p90) cc_final: 0.0206 (p-80) REVERT: G 721 MET cc_start: 0.9190 (mmp) cc_final: 0.8770 (mmm) REVERT: G 865 TYR cc_start: 0.6710 (m-10) cc_final: 0.6365 (m-10) REVERT: H 554 HIS cc_start: 0.2702 (p-80) cc_final: 0.2420 (p-80) REVERT: H 974 ASP cc_start: 0.8814 (t0) cc_final: 0.8377 (m-30) outliers start: 21 outliers final: 7 residues processed: 141 average time/residue: 1.5713 time to fit residues: 253.6751 Evaluate side-chains 138 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 364 GLU 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 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 151 optimal weight: 7.9990 chunk 287 optimal weight: 40.0000 chunk 6 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 264 optimal weight: 0.5980 chunk 194 optimal weight: 10.0000 chunk 263 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 239 optimal weight: 0.8980 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 E 162 ASN F 88 HIS H 683 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.078802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.056302 restraints weight = 99762.079| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.35 r_work: 0.3188 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.006 0.096 24372 Z= 0.381 Angle : 0.676 9.900 33013 Z= 0.328 Chirality : 0.045 0.189 3700 Planarity : 0.004 0.043 4237 Dihedral : 7.104 138.621 3350 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 7.97 % Favored : 90.82 % 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: 0.58 (0.16), residues: 2978 helix: 1.02 (0.14), residues: 1475 sheet: -0.39 (0.25), residues: 408 loop : -0.00 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.012 0.001 HIS H 812 PHE 0.025 0.002 PHE D 375 TYR 0.021 0.002 TYR H 714 ARG 0.004 0.000 ARG H 981 *********************** 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 163 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8454 (tpt) cc_final: 0.8211 (tpt) REVERT: B 283 MET cc_start: 0.8951 (mmt) cc_final: 0.8747 (mmm) REVERT: C 227 MET cc_start: 0.8668 (mmm) cc_final: 0.8205 (mmm) REVERT: C 325 MET cc_start: 0.8792 (mmt) cc_final: 0.8508 (mmm) REVERT: E 47 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5557 (pmm) REVERT: F 305 MET cc_start: 0.8107 (tpp) cc_final: 0.7885 (tpp) REVERT: F 375 PHE cc_start: 0.7624 (t80) cc_final: 0.7271 (t80) REVERT: G 721 MET cc_start: 0.9147 (mmp) cc_final: 0.8637 (mmm) REVERT: G 865 TYR cc_start: 0.6780 (m-10) cc_final: 0.6334 (m-10) REVERT: H 554 HIS cc_start: 0.2777 (p-80) cc_final: 0.2480 (p-80) REVERT: H 974 ASP cc_start: 0.8817 (t0) cc_final: 0.8360 (m-30) outliers start: 31 outliers final: 11 residues processed: 146 average time/residue: 1.5221 time to fit residues: 255.5988 Evaluate side-chains 138 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain G residue 724 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 253 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.080480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.058243 restraints weight = 98823.596| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.33 r_work: 0.3247 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24372 Z= 0.161 Angle : 0.571 8.935 33013 Z= 0.269 Chirality : 0.041 0.172 3700 Planarity : 0.003 0.043 4237 Dihedral : 6.755 126.318 3350 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.97 % Allowed : 9.06 % Favored : 89.96 % 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: 1.01 (0.16), residues: 2978 helix: 1.39 (0.14), residues: 1466 sheet: -0.35 (0.25), residues: 414 loop : 0.27 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 584 HIS 0.005 0.001 HIS H 812 PHE 0.021 0.001 PHE D 375 TYR 0.021 0.001 TYR H 865 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 160 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8413 (tpt) cc_final: 0.8187 (tpt) REVERT: B 123 MET cc_start: 0.8032 (tpp) cc_final: 0.7718 (tpt) REVERT: B 132 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (tmt) REVERT: B 355 MET cc_start: 0.7653 (mtp) cc_final: 0.7372 (ttm) REVERT: C 227 MET cc_start: 0.8382 (mmm) cc_final: 0.8003 (mmm) REVERT: E 44 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8106 (mmm) REVERT: E 82 MET cc_start: 0.8155 (mmm) cc_final: 0.7608 (tpt) REVERT: F 375 PHE cc_start: 0.7497 (t80) cc_final: 0.7189 (t80) REVERT: G 721 MET cc_start: 0.9175 (mmp) cc_final: 0.8806 (mmm) REVERT: H 554 HIS cc_start: 0.2660 (p-80) cc_final: 0.2372 (p-80) REVERT: H 757 PHE cc_start: 0.8854 (m-10) cc_final: 0.8565 (m-80) REVERT: H 974 ASP cc_start: 0.8838 (t0) cc_final: 0.8385 (m-30) outliers start: 25 outliers final: 12 residues processed: 149 average time/residue: 1.5402 time to fit residues: 262.7570 Evaluate side-chains 142 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 5.285 ------------------------------------------------------------------------------- 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 132 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 44 MET 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 733 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 171 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 204 optimal weight: 0.4980 chunk 273 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.057161 restraints weight = 98694.127| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.33 r_work: 0.3216 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 24372 Z= 0.268 Angle : 0.615 9.597 33013 Z= 0.293 Chirality : 0.043 0.168 3700 Planarity : 0.003 0.040 4237 Dihedral : 6.791 128.884 3350 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.09 % Allowed : 9.53 % Favored : 89.38 % 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: 0.98 (0.16), residues: 2978 helix: 1.38 (0.14), residues: 1472 sheet: -0.38 (0.25), residues: 414 loop : 0.24 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.005 0.001 HIS H 812 PHE 0.023 0.001 PHE D 375 TYR 0.021 0.001 TYR H 865 ARG 0.003 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 158 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8410 (tpt) cc_final: 0.8187 (tpt) REVERT: B 123 MET cc_start: 0.8117 (tpp) cc_final: 0.7893 (tpt) REVERT: C 227 MET cc_start: 0.8394 (mmm) cc_final: 0.7959 (mmm) REVERT: C 325 MET cc_start: 0.8714 (mmm) cc_final: 0.8411 (mmt) REVERT: E 82 MET cc_start: 0.8203 (mmm) cc_final: 0.7668 (tpt) REVERT: F 132 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7452 (pp-130) REVERT: F 305 MET cc_start: 0.7492 (tpp) cc_final: 0.6981 (tpp) REVERT: F 375 PHE cc_start: 0.7555 (t80) cc_final: 0.7228 (t80) REVERT: G 721 MET cc_start: 0.9172 (mmp) cc_final: 0.8804 (mmm) REVERT: H 554 HIS cc_start: 0.2861 (p-80) cc_final: 0.2542 (p-80) REVERT: H 974 ASP cc_start: 0.8814 (t0) cc_final: 0.8371 (m-30) outliers start: 28 outliers final: 17 residues processed: 147 average time/residue: 1.5525 time to fit residues: 261.6185 Evaluate side-chains 145 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 2.661 ------------------------------------------------------------------------------- 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 132 MET 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 44 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain G residue 733 MET Chi-restraints excluded: chain H residue 568 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 183 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN D 161 HIS H 812 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.057194 restraints weight = 99026.634| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.35 r_work: 0.3215 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24372 Z= 0.259 Angle : 0.619 10.988 33013 Z= 0.293 Chirality : 0.043 0.172 3700 Planarity : 0.003 0.039 4237 Dihedral : 6.795 129.482 3350 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.21 % Allowed : 9.57 % Favored : 89.23 % 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: 1.02 (0.16), residues: 2978 helix: 1.43 (0.14), residues: 1472 sheet: -0.40 (0.25), residues: 414 loop : 0.25 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS D 371 PHE 0.023 0.001 PHE D 375 TYR 0.022 0.001 TYR H 865 ARG 0.004 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 161 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8419 (tpt) cc_final: 0.8067 (tpt) REVERT: B 123 MET cc_start: 0.8068 (tpp) cc_final: 0.7815 (tpt) REVERT: B 190 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8529 (mtp) REVERT: B 355 MET cc_start: 0.7708 (mtp) cc_final: 0.7323 (ttm) REVERT: C 227 MET cc_start: 0.8439 (mmm) cc_final: 0.8001 (mmm) REVERT: C 325 MET cc_start: 0.8664 (mmm) cc_final: 0.8441 (mmt) REVERT: D 325 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7852 (ttm) REVERT: E 82 MET cc_start: 0.8168 (mmm) cc_final: 0.7637 (tpt) REVERT: F 132 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7477 (pp-130) REVERT: F 305 MET cc_start: 0.7458 (tpp) cc_final: 0.6960 (tpp) REVERT: F 375 PHE cc_start: 0.7572 (t80) cc_final: 0.7222 (t80) REVERT: G 721 MET cc_start: 0.9169 (mmp) cc_final: 0.8759 (mmm) REVERT: H 554 HIS cc_start: 0.2855 (p-80) cc_final: 0.2523 (p-80) REVERT: H 757 PHE cc_start: 0.8859 (m-10) cc_final: 0.8530 (m-80) REVERT: H 974 ASP cc_start: 0.8773 (t0) cc_final: 0.8329 (m-30) outliers start: 31 outliers final: 14 residues processed: 149 average time/residue: 1.5218 time to fit residues: 260.3187 Evaluate side-chains 142 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 190 MET 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 325 MET Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET 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 Chi-restraints excluded: chain G residue 835 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 228 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.078922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.056510 restraints weight = 99071.266| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.35 r_work: 0.3195 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24372 Z= 0.318 Angle : 0.660 11.023 33013 Z= 0.314 Chirality : 0.044 0.185 3700 Planarity : 0.004 0.039 4237 Dihedral : 6.938 135.518 3350 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.28 % Allowed : 9.72 % Favored : 88.99 % 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: 0.98 (0.16), residues: 2978 helix: 1.38 (0.14), residues: 1470 sheet: -0.35 (0.25), residues: 408 loop : 0.21 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS D 87 PHE 0.023 0.001 PHE D 375 TYR 0.022 0.001 TYR H 865 ARG 0.004 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 8 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 to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8398 (tpt) cc_final: 0.8139 (tpt) REVERT: A 355 MET cc_start: 0.8168 (mmm) cc_final: 0.7808 (mmm) REVERT: B 123 MET cc_start: 0.8134 (tpp) cc_final: 0.7918 (tpt) REVERT: B 132 MET cc_start: 0.8413 (tmm) cc_final: 0.8146 (tmt) REVERT: B 190 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: B 355 MET cc_start: 0.7808 (mtp) cc_final: 0.7558 (mtp) REVERT: C 227 MET cc_start: 0.8448 (mmm) cc_final: 0.8000 (mmm) REVERT: E 82 MET cc_start: 0.8249 (mmm) cc_final: 0.7741 (tpt) REVERT: F 132 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7487 (pp-130) REVERT: F 151 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8365 (pt) REVERT: F 305 MET cc_start: 0.7428 (tpp) cc_final: 0.7010 (tpp) REVERT: F 375 PHE cc_start: 0.7647 (t80) cc_final: 0.7252 (t80) REVERT: G 721 MET cc_start: 0.9152 (mmp) cc_final: 0.8888 (mmm) REVERT: G 865 TYR cc_start: 0.6889 (m-10) cc_final: 0.6609 (m-10) REVERT: H 554 HIS cc_start: 0.2947 (p-80) cc_final: 0.2631 (p-80) REVERT: H 757 PHE cc_start: 0.8875 (m-10) cc_final: 0.8564 (m-80) REVERT: H 974 ASP cc_start: 0.8816 (t0) cc_final: 0.8364 (m-30) outliers start: 33 outliers final: 18 residues processed: 147 average time/residue: 1.5209 time to fit residues: 257.1255 Evaluate side-chains 145 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 3.283 ------------------------------------------------------------------------------- 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 190 MET 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 152 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 733 MET Chi-restraints excluded: chain G residue 835 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 236 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 232 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 251 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 198 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.078585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056128 restraints weight = 99248.149| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.31 r_work: 0.3185 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24372 Z= 0.350 Angle : 0.690 14.239 33013 Z= 0.328 Chirality : 0.045 0.189 3700 Planarity : 0.004 0.041 4237 Dihedral : 7.084 141.776 3350 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.21 % Allowed : 10.19 % Favored : 88.60 % 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: 0.88 (0.16), residues: 2978 helix: 1.31 (0.14), residues: 1471 sheet: -0.43 (0.25), residues: 408 loop : 0.18 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS D 87 PHE 0.024 0.002 PHE D 375 TYR 0.023 0.001 TYR H 865 ARG 0.005 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 9 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 159 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8383 (tpt) cc_final: 0.8113 (tpt) REVERT: A 355 MET cc_start: 0.8187 (mmm) cc_final: 0.7985 (mmm) REVERT: B 190 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8612 (mtp) REVERT: B 355 MET cc_start: 0.7838 (mtp) cc_final: 0.7570 (mtp) REVERT: C 227 MET cc_start: 0.8416 (mmm) cc_final: 0.7947 (mmm) REVERT: E 82 MET cc_start: 0.8241 (mmm) cc_final: 0.7735 (tpt) REVERT: E 305 MET cc_start: 0.8846 (mmm) cc_final: 0.8505 (tpp) REVERT: F 305 MET cc_start: 0.7450 (tpp) cc_final: 0.7036 (tpp) REVERT: F 375 PHE cc_start: 0.7660 (t80) cc_final: 0.7278 (t80) REVERT: G 721 MET cc_start: 0.9126 (mmp) cc_final: 0.8873 (mmm) REVERT: G 865 TYR cc_start: 0.6875 (m-10) cc_final: 0.6577 (m-10) REVERT: H 554 HIS cc_start: 0.3040 (p-80) cc_final: 0.2800 (p-80) REVERT: H 757 PHE cc_start: 0.8849 (m-10) cc_final: 0.8529 (m-80) REVERT: H 974 ASP cc_start: 0.8824 (t0) cc_final: 0.8373 (m-30) outliers start: 31 outliers final: 18 residues processed: 150 average time/residue: 1.4948 time to fit residues: 257.9736 Evaluate side-chains 142 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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 190 MET 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 152 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 835 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 196 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 292 optimal weight: 30.0000 chunk 121 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 812 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.079560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.057501 restraints weight = 100086.165| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.30 r_work: 0.3217 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24372 Z= 0.197 Angle : 0.635 14.084 33013 Z= 0.296 Chirality : 0.042 0.185 3700 Planarity : 0.003 0.038 4237 Dihedral : 6.811 129.877 3350 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.66 % Allowed : 10.81 % Favored : 88.53 % 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: 1.15 (0.16), residues: 2978 helix: 1.52 (0.14), residues: 1471 sheet: -0.31 (0.25), residues: 408 loop : 0.31 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.003 0.001 HIS E 161 PHE 0.020 0.001 PHE D 124 TYR 0.023 0.001 TYR G 770 ARG 0.005 0.000 ARG E 28 ********************** REFINEMENT MACRO_CYCLE 10 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 to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8365 (tpt) cc_final: 0.8106 (tpt) REVERT: B 190 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: B 324 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8232 (p) REVERT: B 325 MET cc_start: 0.7897 (mmt) cc_final: 0.7637 (mmt) REVERT: B 355 MET cc_start: 0.7834 (mtp) cc_final: 0.7575 (mtp) REVERT: C 227 MET cc_start: 0.8566 (mmm) cc_final: 0.8098 (mmm) REVERT: E 132 MET cc_start: 0.7274 (pp-130) cc_final: 0.6086 (pp-130) REVERT: F 44 MET cc_start: 0.7793 (ttm) cc_final: 0.7543 (ttt) REVERT: F 305 MET cc_start: 0.7388 (tpp) cc_final: 0.6920 (tpp) REVERT: F 375 PHE cc_start: 0.7657 (t80) cc_final: 0.7223 (t80) REVERT: G 721 MET cc_start: 0.9137 (mmp) cc_final: 0.8884 (mmm) REVERT: G 865 TYR cc_start: 0.6819 (m-10) cc_final: 0.6515 (m-10) REVERT: H 554 HIS cc_start: 0.2986 (p-80) cc_final: 0.2739 (p-80) REVERT: H 682 LYS cc_start: 0.9095 (mppt) cc_final: 0.8350 (tppt) REVERT: H 757 PHE cc_start: 0.8922 (m-10) cc_final: 0.8601 (m-80) REVERT: H 974 ASP cc_start: 0.8854 (t0) cc_final: 0.8430 (m-30) outliers start: 17 outliers final: 11 residues processed: 138 average time/residue: 1.5315 time to fit residues: 244.2595 Evaluate side-chains 135 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 190 MET 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 E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 261 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 174 optimal weight: 6.9990 chunk 283 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.078253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055993 restraints weight = 99540.276| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.31 r_work: 0.3170 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 24372 Z= 0.364 Angle : 0.710 12.267 33013 Z= 0.337 Chirality : 0.045 0.207 3700 Planarity : 0.004 0.039 4237 Dihedral : 7.053 138.505 3350 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.97 % Allowed : 10.54 % Favored : 88.49 % 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: 0.93 (0.16), residues: 2978 helix: 1.35 (0.14), residues: 1472 sheet: -0.42 (0.25), residues: 408 loop : 0.19 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS D 87 PHE 0.023 0.002 PHE D 375 TYR 0.028 0.001 TYR G 770 ARG 0.005 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17874.99 seconds wall clock time: 319 minutes 39.53 seconds (19179.53 seconds total)