Starting phenix.real_space_refine on Mon Aug 25 00:18:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b03_44026/08_2025/9b03_44026.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b03_44026/08_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_44026/08_2025/9b03_44026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b03_44026/08_2025/9b03_44026.map" model { file = "/net/cci-nas-00/data/ceres_data/9b03_44026/08_2025/9b03_44026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b03_44026/08_2025/9b03_44026.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.55, per 1000 atoms: 0.23 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: 1.42 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.00 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: 4.88 Time building geometry restraints manager: 2.07 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: 1.740 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.690 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- 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 24377 Z= 0.262 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG D 210 TYR 0.053 0.002 TYR H 896 PHE 0.033 0.002 PHE F 223 TRP 0.034 0.003 TRP H 569 HIS 0.011 0.001 HIS H 803 Details of bonding type rmsd covalent geometry : bond 0.00514 (24372) covalent geometry : angle 0.96181 (33013) hydrogen bonds : bond 0.16037 ( 1204) hydrogen bonds : angle 6.84708 ( 3330) Misc. bond : bond 0.00352 ( 5) *********************** 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 : 0.646 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: 0.2848 (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: 0.6762 time to fit residues: 125.2544 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 : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 ASN D 115 ASN H 647 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.081064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.058876 restraints weight = 99124.751| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.35 r_work: 0.3255 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24377 Z= 0.174 Angle : 0.622 8.771 33013 Z= 0.302 Chirality : 0.043 0.175 3700 Planarity : 0.004 0.070 4237 Dihedral : 6.915 122.823 3350 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.89 % Allowed : 4.28 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.15), residues: 2978 helix: 0.15 (0.13), residues: 1479 sheet: -0.36 (0.25), residues: 402 loop : -0.10 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.019 0.001 TYR H 714 PHE 0.019 0.002 PHE D 375 TRP 0.016 0.002 TRP A 86 HIS 0.008 0.001 HIS H 812 Details of bonding type rmsd covalent geometry : bond 0.00393 (24372) covalent geometry : angle 0.62154 (33013) hydrogen bonds : bond 0.03454 ( 1204) hydrogen bonds : angle 4.57304 ( 3330) Misc. bond : bond 0.00303 ( 5) *********************** 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 157 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8334 (tpp) cc_final: 0.8125 (tpt) REVERT: B 44 MET cc_start: 0.0797 (OUTLIER) cc_final: -0.0162 (pmt) REVERT: B 132 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7698 (tmt) REVERT: C 132 MET cc_start: 0.8246 (ppp) cc_final: 0.7399 (ttt) REVERT: C 227 MET cc_start: 0.8581 (mmm) cc_final: 0.8131 (mmm) REVERT: F 305 MET cc_start: 0.8156 (mmm) cc_final: 0.7777 (tpp) REVERT: G 554 HIS cc_start: 0.0475 (p90) cc_final: 0.0140 (p-80) REVERT: G 721 MET cc_start: 0.9190 (mmp) cc_final: 0.8519 (mmm) REVERT: H 554 HIS cc_start: 0.2663 (p-80) cc_final: 0.2361 (p-80) REVERT: H 733 MET cc_start: 0.9285 (ptt) cc_final: 0.9061 (tmm) REVERT: H 757 PHE cc_start: 0.8877 (m-10) cc_final: 0.8631 (m-10) REVERT: H 974 ASP cc_start: 0.8894 (t0) cc_final: 0.8429 (m-30) outliers start: 23 outliers final: 2 residues processed: 140 average time/residue: 0.6029 time to fit residues: 96.5741 Evaluate side-chains 131 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain D residue 344 SER 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 236 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 B 101 HIS B 297 ASN C 161 HIS E 40 HIS E 162 ASN F 59 GLN F 88 HIS ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 683 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.078604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055993 restraints weight = 99236.081| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.32 r_work: 0.3181 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 24377 Z= 0.286 Angle : 0.712 10.605 33013 Z= 0.349 Chirality : 0.047 0.187 3700 Planarity : 0.004 0.047 4237 Dihedral : 7.299 144.459 3350 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.44 % Allowed : 6.81 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.16), residues: 2978 helix: 0.71 (0.14), residues: 1475 sheet: -0.46 (0.25), residues: 408 loop : -0.08 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 981 TYR 0.017 0.002 TYR D 143 PHE 0.023 0.002 PHE D 375 TRP 0.016 0.003 TRP D 79 HIS 0.007 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00654 (24372) covalent geometry : angle 0.71193 (33013) hydrogen bonds : bond 0.03919 ( 1204) hydrogen bonds : angle 4.64460 ( 3330) Misc. bond : bond 0.00426 ( 5) *********************** 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 173 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8921 (mmp) cc_final: 0.8661 (mmp) REVERT: A 355 MET cc_start: 0.8080 (mmm) cc_final: 0.7830 (mmm) REVERT: B 123 MET cc_start: 0.8107 (tpp) cc_final: 0.7822 (tpt) REVERT: B 227 MET cc_start: 0.8452 (mmp) cc_final: 0.8241 (mmp) REVERT: C 325 MET cc_start: 0.8803 (mmt) cc_final: 0.8519 (mmm) REVERT: E 47 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5675 (pmm) REVERT: F 44 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7462 (ttm) REVERT: F 132 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6941 (ppp) REVERT: F 305 MET cc_start: 0.8267 (mmm) cc_final: 0.7889 (tpp) REVERT: F 375 PHE cc_start: 0.7687 (t80) cc_final: 0.7345 (t80) REVERT: G 721 MET cc_start: 0.9201 (mmp) cc_final: 0.8940 (mmm) REVERT: G 865 TYR cc_start: 0.6781 (m-10) cc_final: 0.6511 (m-10) REVERT: H 554 HIS cc_start: 0.2803 (p-80) cc_final: 0.2515 (p-80) REVERT: H 733 MET cc_start: 0.9272 (ptt) cc_final: 0.9037 (tmm) REVERT: H 757 PHE cc_start: 0.8910 (m-10) cc_final: 0.8647 (m-10) REVERT: H 974 ASP cc_start: 0.8825 (t0) cc_final: 0.8371 (m-30) outliers start: 37 outliers final: 7 residues processed: 146 average time/residue: 0.7190 time to fit residues: 120.0377 Evaluate side-chains 137 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain G residue 724 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 168 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 0.0050 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- 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 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.080443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.058267 restraints weight = 98631.554| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.31 r_work: 0.3248 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24377 Z= 0.107 Angle : 0.570 8.194 33013 Z= 0.270 Chirality : 0.041 0.170 3700 Planarity : 0.003 0.043 4237 Dihedral : 6.838 128.913 3350 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.97 % Allowed : 8.28 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.16), residues: 2978 helix: 1.20 (0.14), residues: 1475 sheet: -0.39 (0.25), residues: 414 loop : 0.21 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.020 0.001 TYR H 714 PHE 0.023 0.001 PHE D 375 TRP 0.014 0.002 TRP G 584 HIS 0.005 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00241 (24372) covalent geometry : angle 0.56975 (33013) hydrogen bonds : bond 0.02814 ( 1204) hydrogen bonds : angle 4.27077 ( 3330) Misc. bond : bond 0.00256 ( 5) *********************** 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 158 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 227 MET cc_start: 0.8803 (mmp) cc_final: 0.8580 (mmp) REVERT: A 355 MET cc_start: 0.8064 (mmm) cc_final: 0.7823 (mmm) REVERT: B 123 MET cc_start: 0.8100 (tpp) cc_final: 0.7896 (tpt) REVERT: B 132 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7841 (tmt) REVERT: C 132 MET cc_start: 0.8162 (ppp) cc_final: 0.7581 (ttt) REVERT: C 227 MET cc_start: 0.8632 (mmm) cc_final: 0.8119 (mmm) REVERT: C 325 MET cc_start: 0.8689 (mmt) cc_final: 0.8441 (mmm) REVERT: D 44 MET cc_start: 0.5346 (tmm) cc_final: 0.5107 (tmm) REVERT: E 47 MET cc_start: 0.6312 (pmm) cc_final: 0.5447 (pmm) REVERT: F 44 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7182 (ttt) REVERT: F 132 MET cc_start: 0.7679 (ptt) cc_final: 0.7419 (pp-130) REVERT: F 375 PHE cc_start: 0.7505 (t80) cc_final: 0.7183 (t80) REVERT: G 721 MET cc_start: 0.9185 (mmp) cc_final: 0.8646 (mmm) REVERT: G 865 TYR cc_start: 0.6690 (m-10) cc_final: 0.6292 (m-10) REVERT: H 554 HIS cc_start: 0.2712 (p-80) cc_final: 0.2415 (p-80) REVERT: H 733 MET cc_start: 0.9308 (ptt) cc_final: 0.9094 (tmm) REVERT: H 757 PHE cc_start: 0.8911 (m-10) cc_final: 0.8690 (m-10) REVERT: H 974 ASP cc_start: 0.8829 (t0) cc_final: 0.8381 (m-30) outliers start: 25 outliers final: 5 residues processed: 142 average time/residue: 0.6145 time to fit residues: 100.2075 Evaluate side-chains 135 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 MET 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 D residue 344 SER Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain H residue 568 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 117 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 E 115 ASN ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.078227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.055662 restraints weight = 98776.814| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.32 r_work: 0.3170 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 24377 Z= 0.295 Angle : 0.701 11.197 33013 Z= 0.341 Chirality : 0.046 0.191 3700 Planarity : 0.004 0.042 4237 Dihedral : 7.207 145.210 3350 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.44 % Allowed : 9.10 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.16), residues: 2978 helix: 1.10 (0.14), residues: 1481 sheet: -0.46 (0.25), residues: 408 loop : -0.01 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 335 TYR 0.020 0.002 TYR H 865 PHE 0.026 0.002 PHE D 375 TRP 0.016 0.002 TRP D 79 HIS 0.007 0.001 HIS H 812 Details of bonding type rmsd covalent geometry : bond 0.00670 (24372) covalent geometry : angle 0.70115 (33013) hydrogen bonds : bond 0.03671 ( 1204) hydrogen bonds : angle 4.55572 ( 3330) Misc. bond : bond 0.00396 ( 5) *********************** 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 166 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8370 (tpt) cc_final: 0.7896 (tpt) REVERT: A 355 MET cc_start: 0.8052 (mmm) cc_final: 0.7780 (mmm) REVERT: C 227 MET cc_start: 0.8628 (mmm) cc_final: 0.8172 (mmm) REVERT: C 325 MET cc_start: 0.8824 (mmt) cc_final: 0.8519 (mmm) REVERT: D 44 MET cc_start: 0.5577 (tmm) cc_final: 0.5331 (tmm) REVERT: D 325 MET cc_start: 0.8067 (ttm) cc_final: 0.7766 (ttm) REVERT: F 44 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7617 (ttm) REVERT: F 132 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7574 (pp-130) REVERT: F 305 MET cc_start: 0.8156 (tpp) cc_final: 0.7918 (tpp) REVERT: F 375 PHE cc_start: 0.7659 (t80) cc_final: 0.7309 (t80) REVERT: G 721 MET cc_start: 0.9171 (mmp) cc_final: 0.8631 (mmm) REVERT: G 865 TYR cc_start: 0.6884 (m-10) cc_final: 0.6517 (m-10) REVERT: H 554 HIS cc_start: 0.2862 (p-80) cc_final: 0.2564 (p-80) REVERT: H 974 ASP cc_start: 0.8834 (t0) cc_final: 0.8380 (m-30) outliers start: 37 outliers final: 17 residues processed: 149 average time/residue: 0.5912 time to fit residues: 101.5767 Evaluate side-chains 144 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 132 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 C residue 345 ILE 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 148 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain H residue 568 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 181 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 284 optimal weight: 20.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 115 ASN ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.079722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.057320 restraints weight = 98685.254| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.43 r_work: 0.3221 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24377 Z= 0.136 Angle : 0.597 10.446 33013 Z= 0.283 Chirality : 0.042 0.178 3700 Planarity : 0.003 0.040 4237 Dihedral : 6.897 133.975 3350 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 9.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.16), residues: 2978 helix: 1.40 (0.14), residues: 1472 sheet: -0.43 (0.25), residues: 414 loop : 0.22 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 735 TYR 0.021 0.001 TYR H 865 PHE 0.022 0.001 PHE D 375 TRP 0.015 0.002 TRP D 79 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00312 (24372) covalent geometry : angle 0.59729 (33013) hydrogen bonds : bond 0.02904 ( 1204) hydrogen bonds : angle 4.28772 ( 3330) Misc. bond : bond 0.00277 ( 5) *********************** 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 165 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8394 (tpt) cc_final: 0.8052 (tpt) REVERT: A 355 MET cc_start: 0.8076 (mmm) cc_final: 0.7855 (mmm) REVERT: B 132 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7833 (tmm) REVERT: B 190 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8509 (mtp) REVERT: C 227 MET cc_start: 0.8569 (mmm) cc_final: 0.8113 (mmm) REVERT: C 325 MET cc_start: 0.8749 (mmt) cc_final: 0.8460 (mmm) REVERT: D 44 MET cc_start: 0.5505 (tmm) cc_final: 0.5259 (tmm) REVERT: D 325 MET cc_start: 0.7990 (ttm) cc_final: 0.7702 (ttm) REVERT: E 44 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8194 (mmm) REVERT: F 44 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7393 (ttt) REVERT: F 375 PHE cc_start: 0.7657 (t80) cc_final: 0.7309 (t80) REVERT: G 721 MET cc_start: 0.9196 (mmp) cc_final: 0.8642 (mmm) REVERT: G 865 TYR cc_start: 0.6928 (m-10) cc_final: 0.6574 (m-10) REVERT: H 554 HIS cc_start: 0.2697 (p-80) cc_final: 0.2401 (p-80) REVERT: H 974 ASP cc_start: 0.8766 (t0) cc_final: 0.8338 (m-30) outliers start: 34 outliers final: 13 residues processed: 148 average time/residue: 0.5806 time to fit residues: 98.7392 Evaluate side-chains 144 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP 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 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 355 MET Chi-restraints excluded: chain F residue 44 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 252 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 290 optimal weight: 40.0000 chunk 258 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 ** H 812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.079192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.056706 restraints weight = 99239.636| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.29 r_work: 0.3206 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24377 Z= 0.181 Angle : 0.627 10.444 33013 Z= 0.297 Chirality : 0.043 0.177 3700 Planarity : 0.003 0.040 4237 Dihedral : 6.892 133.686 3350 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.36 % Allowed : 9.72 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.16), residues: 2978 helix: 1.43 (0.14), residues: 1470 sheet: -0.45 (0.25), residues: 414 loop : 0.22 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 28 TYR 0.022 0.001 TYR H 865 PHE 0.022 0.001 PHE D 375 TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00416 (24372) covalent geometry : angle 0.62697 (33013) hydrogen bonds : bond 0.03077 ( 1204) hydrogen bonds : angle 4.30637 ( 3330) Misc. bond : bond 0.00296 ( 5) *********************** 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 163 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8432 (tpt) cc_final: 0.8130 (tpt) REVERT: A 355 MET cc_start: 0.8064 (mmm) cc_final: 0.7777 (mmm) REVERT: B 123 MET cc_start: 0.7922 (tpp) cc_final: 0.7479 (tpp) REVERT: B 190 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8557 (mtp) REVERT: C 227 MET cc_start: 0.8654 (mmm) cc_final: 0.8221 (mmm) REVERT: C 325 MET cc_start: 0.8807 (mmt) cc_final: 0.8512 (mmm) REVERT: D 44 MET cc_start: 0.5619 (tmm) cc_final: 0.5293 (tmm) REVERT: D 325 MET cc_start: 0.8011 (ttm) cc_final: 0.7659 (ttm) REVERT: F 44 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7440 (ttt) REVERT: F 151 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8347 (pt) REVERT: F 305 MET cc_start: 0.8328 (mmm) cc_final: 0.7826 (mpp) REVERT: F 375 PHE cc_start: 0.7615 (t80) cc_final: 0.7249 (t80) REVERT: G 721 MET cc_start: 0.9168 (mmp) cc_final: 0.8532 (mmm) REVERT: G 865 TYR cc_start: 0.6789 (m-10) cc_final: 0.6373 (m-10) REVERT: H 554 HIS cc_start: 0.3045 (p-80) cc_final: 0.2726 (p-80) REVERT: H 974 ASP cc_start: 0.8787 (t0) cc_final: 0.8347 (m-30) outliers start: 35 outliers final: 19 residues processed: 149 average time/residue: 0.6104 time to fit residues: 104.2034 Evaluate side-chains 146 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP 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 190 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 132 MET 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 355 MET Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 835 ILE Chi-restraints excluded: chain H residue 568 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 187 optimal weight: 3.9990 chunk 281 optimal weight: 30.0000 chunk 298 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 192 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3949 r_free = 0.3949 target = 0.079777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.057468 restraints weight = 98752.463| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.40 r_work: 0.3225 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24377 Z= 0.137 Angle : 0.606 11.539 33013 Z= 0.284 Chirality : 0.042 0.177 3700 Planarity : 0.003 0.039 4237 Dihedral : 6.755 127.593 3350 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.13 % Allowed : 10.04 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.16), residues: 2978 helix: 1.58 (0.14), residues: 1464 sheet: -0.38 (0.25), residues: 414 loop : 0.28 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 28 TYR 0.023 0.001 TYR H 865 PHE 0.021 0.001 PHE D 375 TRP 0.014 0.002 TRP D 79 HIS 0.003 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00315 (24372) covalent geometry : angle 0.60614 (33013) hydrogen bonds : bond 0.02845 ( 1204) hydrogen bonds : angle 4.23142 ( 3330) Misc. bond : bond 0.00251 ( 5) *********************** 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 157 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8424 (tpt) cc_final: 0.8167 (tpt) REVERT: A 355 MET cc_start: 0.8032 (mmm) cc_final: 0.7830 (mmm) REVERT: B 132 MET cc_start: 0.8254 (tmm) cc_final: 0.8009 (tmm) REVERT: B 190 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8534 (mtp) REVERT: B 355 MET cc_start: 0.7789 (mtp) cc_final: 0.7467 (ttm) REVERT: C 227 MET cc_start: 0.8582 (mmm) cc_final: 0.8045 (mmm) REVERT: C 325 MET cc_start: 0.8757 (mmt) cc_final: 0.8488 (mmm) REVERT: D 44 MET cc_start: 0.5687 (tmm) cc_final: 0.5344 (tmm) REVERT: F 44 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7381 (ttt) REVERT: F 151 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8409 (pt) REVERT: F 305 MET cc_start: 0.8425 (mmm) cc_final: 0.7951 (mpp) REVERT: F 375 PHE cc_start: 0.7641 (t80) cc_final: 0.7267 (t80) REVERT: G 721 MET cc_start: 0.9176 (mmp) cc_final: 0.8783 (mmm) REVERT: G 902 GLN cc_start: 0.8976 (mp10) cc_final: 0.8764 (pm20) REVERT: H 554 HIS cc_start: 0.2870 (p-80) cc_final: 0.2562 (p-80) REVERT: H 974 ASP cc_start: 0.8885 (t0) cc_final: 0.8415 (m-30) outliers start: 29 outliers final: 11 residues processed: 148 average time/residue: 0.5982 time to fit residues: 101.2257 Evaluate side-chains 139 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 364 GLU 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 148 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 151 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 124 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 277 optimal weight: 40.0000 chunk 80 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.079693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.057285 restraints weight = 99830.850| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.36 r_work: 0.3223 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24377 Z= 0.146 Angle : 0.623 12.114 33013 Z= 0.291 Chirality : 0.042 0.179 3700 Planarity : 0.003 0.038 4237 Dihedral : 6.708 124.564 3350 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.05 % Allowed : 10.31 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.16), residues: 2978 helix: 1.58 (0.14), residues: 1470 sheet: -0.38 (0.25), residues: 414 loop : 0.33 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 28 TYR 0.021 0.001 TYR H 865 PHE 0.020 0.001 PHE D 375 TRP 0.014 0.002 TRP D 79 HIS 0.003 0.001 HIS D 87 Details of bonding type rmsd covalent geometry : bond 0.00336 (24372) covalent geometry : angle 0.62266 (33013) hydrogen bonds : bond 0.02881 ( 1204) hydrogen bonds : angle 4.23980 ( 3330) Misc. bond : bond 0.00259 ( 5) *********************** 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 153 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8430 (tpt) cc_final: 0.8172 (tpt) REVERT: A 355 MET cc_start: 0.8048 (mmm) cc_final: 0.7787 (mmm) REVERT: B 190 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8536 (mtp) REVERT: B 355 MET cc_start: 0.7737 (mtp) cc_final: 0.7398 (ttm) REVERT: C 227 MET cc_start: 0.8666 (mmm) cc_final: 0.8107 (mmm) REVERT: C 325 MET cc_start: 0.8765 (mmt) cc_final: 0.8498 (mmm) REVERT: D 44 MET cc_start: 0.5672 (tmm) cc_final: 0.5418 (tmm) REVERT: F 44 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7408 (ttt) REVERT: F 151 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8409 (pt) REVERT: F 305 MET cc_start: 0.8440 (mmm) cc_final: 0.7999 (tpp) REVERT: F 375 PHE cc_start: 0.7617 (t80) cc_final: 0.7232 (t80) REVERT: G 721 MET cc_start: 0.9143 (mmp) cc_final: 0.8765 (mmm) REVERT: H 554 HIS cc_start: 0.2879 (p-80) cc_final: 0.2617 (p-80) REVERT: H 682 LYS cc_start: 0.9013 (mppt) cc_final: 0.8245 (tppt) REVERT: H 757 PHE cc_start: 0.8880 (m-10) cc_final: 0.8583 (m-80) REVERT: H 974 ASP cc_start: 0.8856 (t0) cc_final: 0.8429 (m-30) outliers start: 27 outliers final: 16 residues processed: 145 average time/residue: 0.6323 time to fit residues: 105.3394 Evaluate side-chains 143 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP 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 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 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 835 ILE Chi-restraints excluded: chain H residue 568 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 9 optimal weight: 10.0000 chunk 287 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 277 optimal weight: 40.0000 chunk 132 optimal weight: 5.9990 chunk 162 optimal weight: 0.0030 chunk 275 optimal weight: 8.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 812 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.079863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.057808 restraints weight = 100080.535| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.37 r_work: 0.3226 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24377 Z= 0.122 Angle : 0.622 16.624 33013 Z= 0.288 Chirality : 0.042 0.191 3700 Planarity : 0.003 0.039 4237 Dihedral : 6.582 117.409 3350 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.82 % Allowed : 10.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.16), residues: 2978 helix: 1.67 (0.14), residues: 1465 sheet: -0.34 (0.25), residues: 414 loop : 0.37 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 28 TYR 0.023 0.001 TYR G 770 PHE 0.020 0.001 PHE D 124 TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00280 (24372) covalent geometry : angle 0.62247 (33013) hydrogen bonds : bond 0.02757 ( 1204) hydrogen bonds : angle 4.19486 ( 3330) Misc. bond : bond 0.00234 ( 5) ********************** 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 147 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8425 (tpt) cc_final: 0.8177 (tpt) REVERT: B 132 MET cc_start: 0.8155 (tmm) cc_final: 0.7700 (tmm) REVERT: B 190 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: B 355 MET cc_start: 0.7804 (mtp) cc_final: 0.7487 (ttm) REVERT: C 227 MET cc_start: 0.8660 (mmm) cc_final: 0.8131 (mmm) REVERT: C 325 MET cc_start: 0.8695 (mmt) cc_final: 0.8446 (mmm) REVERT: D 44 MET cc_start: 0.5625 (tmm) cc_final: 0.5290 (tmm) REVERT: F 44 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7372 (ttt) REVERT: F 151 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8453 (pt) REVERT: F 305 MET cc_start: 0.8452 (mmm) cc_final: 0.8015 (tpp) REVERT: F 375 PHE cc_start: 0.7621 (t80) cc_final: 0.7217 (t80) REVERT: G 721 MET cc_start: 0.9146 (mmp) cc_final: 0.8892 (mmm) REVERT: G 865 TYR cc_start: 0.6813 (m-10) cc_final: 0.6515 (m-10) REVERT: H 554 HIS cc_start: 0.2918 (p-80) cc_final: 0.2640 (p-80) REVERT: H 682 LYS cc_start: 0.9087 (mppt) cc_final: 0.8356 (tppt) REVERT: H 757 PHE cc_start: 0.8911 (m-10) cc_final: 0.8604 (m-80) REVERT: H 974 ASP cc_start: 0.8872 (t0) cc_final: 0.8465 (m-30) outliers start: 21 outliers final: 16 residues processed: 143 average time/residue: 0.6344 time to fit residues: 104.0457 Evaluate side-chains 143 residues out of total 2571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP 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 86 TRP 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 152 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 835 ILE Chi-restraints excluded: chain H residue 568 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 33 optimal weight: 8.9990 chunk 261 optimal weight: 0.0050 chunk 234 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 239 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 194 optimal weight: 0.0020 chunk 180 optimal weight: 0.0670 chunk 158 optimal weight: 2.9990 chunk 274 optimal weight: 30.0000 overall best weight: 0.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS E 173 HIS F 173 HIS H 812 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.081173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.059299 restraints weight = 99730.392| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.34 r_work: 0.3273 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24377 Z= 0.093 Angle : 0.601 16.742 33013 Z= 0.277 Chirality : 0.041 0.178 3700 Planarity : 0.003 0.037 4237 Dihedral : 6.263 105.023 3350 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.51 % Allowed : 11.09 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.16), residues: 2978 helix: 1.88 (0.14), residues: 1462 sheet: -0.19 (0.25), residues: 414 loop : 0.47 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 28 TYR 0.024 0.001 TYR G 770 PHE 0.017 0.001 PHE D 124 TRP 0.016 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00211 (24372) covalent geometry : angle 0.60096 (33013) hydrogen bonds : bond 0.02507 ( 1204) hydrogen bonds : angle 4.05507 ( 3330) Misc. bond : bond 0.00180 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8403.75 seconds wall clock time: 143 minutes 43.13 seconds (8623.13 seconds total)