Starting phenix.real_space_refine on Thu Aug 8 18:18:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9azq_44019/08_2024/9azq_44019.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9azq_44019/08_2024/9azq_44019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9azq_44019/08_2024/9azq_44019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9azq_44019/08_2024/9azq_44019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9azq_44019/08_2024/9azq_44019.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9azq_44019/08_2024/9azq_44019.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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 14 5.49 5 Mg 7 5.21 5 S 160 5.16 5 C 14863 2.51 5 N 3996 2.21 5 O 4523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23563 Number of models: 1 Model: "" Number of chains: 16 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: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 483 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 7, 'TRANS': 52} Chain: "H" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2584 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 314} Chain: "I" 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: "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} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.11, per 1000 atoms: 0.56 Number of scatterers: 23563 At special positions: 0 Unit cell: (103.68, 115.56, 247.32, 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 160 16.00 P 14 15.00 Mg 7 11.99 O 4523 8.00 N 3996 7.00 C 14863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.22 Conformation dependent library (CDL) restraints added in 4.3 seconds 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 41 sheets defined 52.1% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.892A 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 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.854A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.537A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.525A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 4.168A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.519A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 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: 3.657A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.155A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.519A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.925A 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 368 through 374 removed outlier: 4.200A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.639A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.911A 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: 3.942A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.777A 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 193 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.889A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.052A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 removed outlier: 3.576A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 267' Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.072A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.527A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 removed outlier: 3.631A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.883A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.252A 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 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.592A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.811A 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 125 removed outlier: 3.844A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.788A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.540A 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 263 removed outlier: 3.734A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 4.481A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 removed outlier: 3.531A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 267' Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.556A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.040A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.805A 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: 3.954A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.787A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.913A 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 removed outlier: 3.667A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.575A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.531A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.670A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.858A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.666A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.518A pdb=" N LEU D 293 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.009A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 3.765A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.820A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.931A 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 193 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.568A pdb=" N GLU E 226 " --> pdb=" O ASP E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.817A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.711A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.037A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.914A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.967A 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 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.734A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.733A 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: 3.688A 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 202 through 216 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 263 removed outlier: 3.629A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix removed outlier: 4.624A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 267 removed outlier: 3.676A pdb=" N ILE F 267 " --> pdb=" O PRO F 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 264 through 267' Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.719A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.687A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.605A pdb=" N PHE F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 349 through 353' Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 3.974A 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 583 through 588 removed outlier: 4.039A 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 'H' and resid 634 through 647 removed outlier: 3.540A pdb=" N SER H 638 " --> pdb=" O ASP H 634 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS H 646 " --> pdb=" O ASN H 642 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 662 removed outlier: 3.514A pdb=" N VAL H 655 " --> pdb=" O SER H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 Processing helix chain 'H' and resid 681 through 690 Processing helix chain 'H' and resid 694 through 698 Processing helix chain 'H' and resid 699 through 711 removed outlier: 3.570A pdb=" N ILE H 711 " --> pdb=" O LEU H 707 " (cutoff:3.500A) Processing helix chain 'H' and resid 713 through 750 Proline residue: H 736 - end of helix Processing helix chain 'H' and resid 753 through 769 Processing helix chain 'H' and resid 781 through 785 removed outlier: 3.531A pdb=" N LEU H 785 " --> pdb=" O ILE H 782 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 811 removed outlier: 3.837A pdb=" N LYS H 810 " --> pdb=" O GLU H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 816 removed outlier: 3.650A pdb=" N LEU H 815 " --> pdb=" O HIS H 812 " (cutoff:3.500A) Processing helix chain 'H' and resid 817 through 822 removed outlier: 3.919A pdb=" N ASP H 821 " --> pdb=" O GLN H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 832 through 856 Processing helix chain 'H' and resid 858 through 897 removed outlier: 5.831A pdb=" N GLU H 867 " --> pdb=" O GLU H 863 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG H 868 " --> pdb=" O GLN H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 906 through 947 Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.792A pdb=" N GLU I 100 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 97 through 101' Processing helix chain 'I' and resid 112 through 125 removed outlier: 4.059A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 146 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 194 through 196 No H-bonds generated for 'chain 'I' and resid 194 through 196' Processing helix chain 'I' and resid 202 through 216 removed outlier: 3.704A pdb=" N GLU I 207 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE I 208 " --> pdb=" O ALA I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.670A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 removed outlier: 3.843A pdb=" N PHE I 262 " --> pdb=" O PRO I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 264 through 267 removed outlier: 3.523A pdb=" N ILE I 267 " --> pdb=" O PRO I 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 264 through 267' Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 289 through 296 Processing helix chain 'I' and resid 302 through 306 removed outlier: 4.192A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 348 Processing helix chain 'I' and resid 350 through 355 removed outlier: 3.880A pdb=" N GLN I 354 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 Processing helix chain 'I' and resid 368 through 374 removed outlier: 4.208A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.557A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (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: 6.481A 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: 4.152A 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: 6.546A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.451A 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 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.309A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (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: 6.476A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.705A 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 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.518A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (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: 6.427A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (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: 6.379A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.703A 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: 4.151A 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: 6.536A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (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 169 through 170 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.319A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.665A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 removed outlier: 3.717A pdb=" N SER F 155 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD9, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.404A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR I 133 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET I 132 " --> pdb=" O ILE I 357 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AE2, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AE3, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.376A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 238 through 241 1146 hydrogen bonds defined for protein. 3114 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.81 Time building geometry restraints manager: 10.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6244 1.33 - 1.45: 4273 1.45 - 1.57: 13240 1.57 - 1.69: 23 1.69 - 1.81: 278 Bond restraints: 24058 Sorted by residual: bond pdb=" CA VAL G 551 " pdb=" C VAL G 551 " ideal model delta sigma weight residual 1.525 1.604 -0.079 2.10e-02 2.27e+03 1.42e+01 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" CE1 HIC I 73 " pdb=" NE2 HIC I 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.88e+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 7.75e+00 ... (remaining 24053 not shown) Histogram of bond angle deviations from ideal: 98.56 - 106.17: 768 106.17 - 113.79: 13578 113.79 - 121.40: 12062 121.40 - 129.02: 6049 129.02 - 136.64: 165 Bond angle restraints: 32622 Sorted by residual: angle pdb=" C GLU H 629 " pdb=" N ILE H 630 " pdb=" CA ILE H 630 " ideal model delta sigma weight residual 121.97 132.40 -10.43 1.80e+00 3.09e-01 3.36e+01 angle pdb=" N ASN A 128 " pdb=" CA ASN A 128 " pdb=" C ASN A 128 " ideal model delta sigma weight residual 110.30 118.30 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" CA VAL G 551 " pdb=" C VAL G 551 " pdb=" N PRO G 552 " ideal model delta sigma weight residual 116.90 124.02 -7.12 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C ALA H 828 " pdb=" CA ALA H 828 " pdb=" CB ALA H 828 " ideal model delta sigma weight residual 115.79 110.15 5.64 1.19e+00 7.06e-01 2.24e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 122.08 128.74 -6.66 1.47e+00 4.63e-01 2.05e+01 ... (remaining 32617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 14328 35.99 - 71.97: 197 71.97 - 107.96: 13 107.96 - 143.94: 8 143.94 - 179.93: 8 Dihedral angle restraints: 14554 sinusoidal: 5912 harmonic: 8642 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 119.93 -179.93 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP I 401 " pdb=" O5' ADP I 401 " pdb=" PA ADP I 401 " pdb=" O2A ADP I 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.94 -167.94 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.68 -167.68 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 14551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3093 0.072 - 0.143: 473 0.143 - 0.215: 53 0.215 - 0.286: 14 0.286 - 0.358: 3 Chirality restraints: 3636 Sorted by residual: chirality pdb=" CB VAL G 551 " pdb=" CA VAL G 551 " pdb=" CG1 VAL G 551 " pdb=" CG2 VAL G 551 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ASN A 128 " pdb=" N ASN A 128 " pdb=" C ASN A 128 " pdb=" CB ASN A 128 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE H 630 " pdb=" CA ILE H 630 " pdb=" CG1 ILE H 630 " pdb=" CG2 ILE H 630 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3633 not shown) Planarity restraints: 4179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 824 " 0.058 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO H 825 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO H 825 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 825 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.051 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO D 243 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " 0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO E 112 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " 0.041 5.00e-02 4.00e+02 ... (remaining 4176 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 320 2.64 - 3.20: 19409 3.20 - 3.77: 37672 3.77 - 4.33: 52864 4.33 - 4.90: 84629 Nonbonded interactions: 194894 Sorted by model distance: nonbonded pdb=" O2B ADP F 401 " pdb="MG MG F 402 " model vdw 2.075 2.170 nonbonded pdb=" O3A ADP A 401 " pdb="MG MG A 402 " model vdw 2.087 2.170 nonbonded pdb=" O2A ADP B 401 " pdb="MG MG B 402 " model vdw 2.107 2.170 nonbonded pdb=" O3B ADP B 401 " pdb="MG MG B 402 " model vdw 2.108 2.170 nonbonded pdb=" O1B ADP I 401 " pdb="MG MG I 402 " model vdw 2.114 2.170 ... (remaining 194889 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' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 22.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 63.190 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 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 0.095 24058 Z= 0.314 Angle : 0.880 11.117 32622 Z= 0.481 Chirality : 0.054 0.358 3636 Planarity : 0.008 0.086 4179 Dihedral : 15.038 179.931 9000 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.13), residues: 2941 helix: -2.64 (0.09), residues: 1382 sheet: -0.83 (0.22), residues: 462 loop : -1.04 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 569 HIS 0.010 0.001 HIS I 40 PHE 0.027 0.002 PHE B 124 TYR 0.023 0.002 TYR H 705 ARG 0.006 0.001 ARG H 837 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9385 (tpt) cc_final: 0.8834 (tpt) REVERT: A 123 MET cc_start: 0.9485 (mmp) cc_final: 0.9188 (mmm) REVERT: A 257 CYS cc_start: 0.9546 (t) cc_final: 0.9287 (p) REVERT: A 299 MET cc_start: 0.8675 (mtm) cc_final: 0.8353 (ptp) REVERT: A 313 MET cc_start: 0.9570 (tpp) cc_final: 0.9027 (tpp) REVERT: A 325 MET cc_start: 0.8780 (mmm) cc_final: 0.8160 (mpp) REVERT: A 355 MET cc_start: 0.8945 (mtp) cc_final: 0.8744 (tpt) REVERT: B 72 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9066 (mp0) REVERT: B 82 MET cc_start: 0.9231 (tpt) cc_final: 0.8411 (tpt) REVERT: B 227 MET cc_start: 0.9149 (mmm) cc_final: 0.8850 (mmm) REVERT: B 355 MET cc_start: 0.8976 (mtp) cc_final: 0.8405 (tpp) REVERT: C 311 ASP cc_start: 0.9291 (m-30) cc_final: 0.9061 (p0) REVERT: C 355 MET cc_start: 0.9410 (mtp) cc_final: 0.9063 (mtp) REVERT: D 82 MET cc_start: 0.8986 (tpt) cc_final: 0.8622 (tpt) REVERT: D 325 MET cc_start: 0.8974 (mmt) cc_final: 0.8745 (mmm) REVERT: E 82 MET cc_start: 0.9394 (tpt) cc_final: 0.8633 (tpt) REVERT: E 283 MET cc_start: 0.9462 (mmm) cc_final: 0.9256 (mmm) REVERT: E 299 MET cc_start: 0.8682 (mtm) cc_final: 0.7877 (mmp) REVERT: E 305 MET cc_start: 0.9532 (mmm) cc_final: 0.9322 (mmm) REVERT: E 313 MET cc_start: 0.9467 (tpp) cc_final: 0.9113 (tpp) REVERT: E 325 MET cc_start: 0.8542 (mmm) cc_final: 0.8250 (mpp) REVERT: E 355 MET cc_start: 0.9328 (mtp) cc_final: 0.9063 (mtp) REVERT: F 82 MET cc_start: 0.9482 (tpt) cc_final: 0.9073 (tpp) REVERT: F 190 MET cc_start: 0.8780 (mtp) cc_final: 0.8524 (mmm) REVERT: F 299 MET cc_start: 0.5634 (mtm) cc_final: 0.5153 (ptt) REVERT: F 313 MET cc_start: 0.9656 (tpp) cc_final: 0.9455 (tpp) REVERT: G 583 MET cc_start: 0.0790 (ttm) cc_final: 0.0240 (mpp) REVERT: H 694 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8832 (tm-30) REVERT: H 812 HIS cc_start: 0.7021 (m90) cc_final: 0.6471 (t-170) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3738 time to fit residues: 121.3527 Evaluate side-chains 145 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 151 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 111 ASN ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 832 ASN H 864 GLN I 173 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24058 Z= 0.227 Angle : 0.646 11.489 32622 Z= 0.314 Chirality : 0.042 0.165 3636 Planarity : 0.005 0.068 4179 Dihedral : 11.019 174.711 3330 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.32 % Allowed : 4.00 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2941 helix: -0.13 (0.13), residues: 1335 sheet: -0.48 (0.23), residues: 455 loop : -0.04 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 569 HIS 0.009 0.001 HIS H 703 PHE 0.013 0.001 PHE I 352 TYR 0.012 0.001 TYR I 53 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8471 (tpp) cc_final: 0.8056 (tpp) REVERT: A 82 MET cc_start: 0.9440 (tpt) cc_final: 0.8859 (tpt) REVERT: A 119 MET cc_start: 0.9712 (ttp) cc_final: 0.8961 (tmm) REVERT: A 123 MET cc_start: 0.9588 (mmp) cc_final: 0.9209 (mmm) REVERT: A 132 MET cc_start: 0.9243 (tmm) cc_final: 0.8835 (tmm) REVERT: A 257 CYS cc_start: 0.9664 (t) cc_final: 0.9377 (t) REVERT: A 269 MET cc_start: 0.8955 (mtp) cc_final: 0.8548 (mtp) REVERT: A 299 MET cc_start: 0.8672 (mtm) cc_final: 0.8063 (ptm) REVERT: A 325 MET cc_start: 0.8730 (mmm) cc_final: 0.8498 (mmm) REVERT: B 123 MET cc_start: 0.9222 (mmm) cc_final: 0.8955 (mmm) REVERT: B 227 MET cc_start: 0.9114 (mmm) cc_final: 0.8834 (mmm) REVERT: B 299 MET cc_start: 0.8216 (ptm) cc_final: 0.7836 (ptm) REVERT: B 355 MET cc_start: 0.8954 (mtp) cc_final: 0.8411 (mmm) REVERT: C 44 MET cc_start: 0.8873 (mpp) cc_final: 0.8559 (mmp) REVERT: C 82 MET cc_start: 0.8813 (tpt) cc_final: 0.8305 (tpt) REVERT: C 355 MET cc_start: 0.9451 (mtp) cc_final: 0.9073 (mtp) REVERT: D 47 MET cc_start: 0.6371 (ptm) cc_final: 0.5752 (ppp) REVERT: D 82 MET cc_start: 0.9111 (tpt) cc_final: 0.8687 (tpt) REVERT: D 104 LEU cc_start: 0.9199 (tt) cc_final: 0.8998 (pp) REVERT: D 305 MET cc_start: 0.8899 (mmm) cc_final: 0.8673 (mmm) REVERT: D 325 MET cc_start: 0.9154 (mmt) cc_final: 0.8557 (mmm) REVERT: E 82 MET cc_start: 0.9504 (tpt) cc_final: 0.8907 (tpp) REVERT: E 119 MET cc_start: 0.9260 (ptm) cc_final: 0.8983 (ptt) REVERT: E 299 MET cc_start: 0.8733 (mtm) cc_final: 0.7967 (mmp) REVERT: E 313 MET cc_start: 0.9414 (tpp) cc_final: 0.9207 (tpp) REVERT: E 325 MET cc_start: 0.8538 (mmm) cc_final: 0.8088 (mmm) REVERT: F 82 MET cc_start: 0.9560 (tpt) cc_final: 0.9023 (tpt) REVERT: F 269 MET cc_start: 0.7991 (ttt) cc_final: 0.7678 (ttt) REVERT: G 583 MET cc_start: 0.0729 (ttm) cc_final: 0.0326 (mpp) REVERT: H 694 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8794 (tp30) REVERT: H 812 HIS cc_start: 0.7279 (m90) cc_final: 0.6675 (t-170) REVERT: I 47 MET cc_start: 0.4154 (mpp) cc_final: 0.3934 (mpp) REVERT: I 82 MET cc_start: 0.9295 (mmm) cc_final: 0.9003 (mmm) REVERT: I 113 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8005 (tppt) outliers start: 8 outliers final: 4 residues processed: 150 average time/residue: 0.3384 time to fit residues: 81.4559 Evaluate side-chains 141 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 41 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 20.0000 chunk 83 optimal weight: 0.3980 chunk 224 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN D 173 HIS ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24058 Z= 0.228 Angle : 0.638 8.863 32622 Z= 0.308 Chirality : 0.042 0.176 3636 Planarity : 0.004 0.066 4179 Dihedral : 10.060 179.101 3330 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.44 % Allowed : 4.79 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2941 helix: 0.63 (0.14), residues: 1336 sheet: -0.21 (0.24), residues: 455 loop : 0.24 (0.20), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 79 HIS 0.006 0.001 HIS H 703 PHE 0.013 0.001 PHE B 352 TYR 0.013 0.001 TYR B 69 ARG 0.013 0.000 ARG H 820 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8466 (tpp) cc_final: 0.7981 (tpp) REVERT: A 47 MET cc_start: 0.5102 (ptt) cc_final: 0.4898 (ptt) REVERT: A 82 MET cc_start: 0.9439 (tpt) cc_final: 0.8942 (tpt) REVERT: A 119 MET cc_start: 0.9727 (ttp) cc_final: 0.8964 (tmm) REVERT: A 123 MET cc_start: 0.9633 (mmp) cc_final: 0.9208 (mmm) REVERT: A 132 MET cc_start: 0.9333 (tmm) cc_final: 0.8979 (tmm) REVERT: A 257 CYS cc_start: 0.9670 (t) cc_final: 0.9413 (t) REVERT: A 299 MET cc_start: 0.8571 (mtm) cc_final: 0.8236 (mmp) REVERT: A 305 MET cc_start: 0.8820 (mmm) cc_final: 0.8472 (mmm) REVERT: A 355 MET cc_start: 0.9333 (mmm) cc_final: 0.8721 (tpp) REVERT: B 123 MET cc_start: 0.9299 (mmm) cc_final: 0.8990 (mmm) REVERT: B 227 MET cc_start: 0.9107 (mmm) cc_final: 0.8846 (mmm) REVERT: B 299 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7784 (ptm) REVERT: B 355 MET cc_start: 0.8897 (mtp) cc_final: 0.8326 (mmm) REVERT: C 44 MET cc_start: 0.8804 (mpp) cc_final: 0.8589 (mmp) REVERT: C 82 MET cc_start: 0.8826 (tpt) cc_final: 0.8270 (tpt) REVERT: C 305 MET cc_start: 0.8085 (mmt) cc_final: 0.7714 (mmt) REVERT: C 313 MET cc_start: 0.9247 (mmm) cc_final: 0.9001 (mmm) REVERT: C 355 MET cc_start: 0.9419 (mtp) cc_final: 0.9190 (mtp) REVERT: D 82 MET cc_start: 0.9135 (tpt) cc_final: 0.8705 (tpt) REVERT: D 132 MET cc_start: 0.8611 (ppp) cc_final: 0.8209 (ppp) REVERT: D 227 MET cc_start: 0.9162 (mmm) cc_final: 0.8803 (mmm) REVERT: D 305 MET cc_start: 0.8842 (mmm) cc_final: 0.8563 (mmm) REVERT: D 325 MET cc_start: 0.9151 (mmt) cc_final: 0.8423 (mmm) REVERT: E 82 MET cc_start: 0.9509 (tpt) cc_final: 0.8916 (tpp) REVERT: E 190 MET cc_start: 0.8994 (tmm) cc_final: 0.8759 (tmm) REVERT: E 299 MET cc_start: 0.8783 (mtm) cc_final: 0.8008 (mmp) REVERT: E 313 MET cc_start: 0.9402 (tpp) cc_final: 0.9182 (tpp) REVERT: E 325 MET cc_start: 0.8552 (mmm) cc_final: 0.8075 (mmm) REVERT: F 82 MET cc_start: 0.9580 (tpt) cc_final: 0.9027 (tpt) REVERT: F 269 MET cc_start: 0.7988 (ttt) cc_final: 0.7730 (ttt) REVERT: H 694 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8844 (tp30) REVERT: H 812 HIS cc_start: 0.6978 (m90) cc_final: 0.6268 (t70) REVERT: I 82 MET cc_start: 0.9416 (mmm) cc_final: 0.9110 (mmm) outliers start: 11 outliers final: 6 residues processed: 146 average time/residue: 0.3638 time to fit residues: 85.0167 Evaluate side-chains 143 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain F residue 41 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 141 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24058 Z= 0.285 Angle : 0.677 8.331 32622 Z= 0.330 Chirality : 0.042 0.182 3636 Planarity : 0.004 0.061 4179 Dihedral : 9.359 177.888 3330 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.75 % Allowed : 6.49 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2941 helix: 0.82 (0.14), residues: 1334 sheet: -0.14 (0.25), residues: 455 loop : 0.31 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 79 HIS 0.006 0.001 HIS D 173 PHE 0.013 0.001 PHE E 200 TYR 0.013 0.002 TYR C 337 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8460 (tpp) cc_final: 0.8127 (tpp) REVERT: A 82 MET cc_start: 0.9471 (tpt) cc_final: 0.8948 (tpt) REVERT: A 119 MET cc_start: 0.9739 (ttp) cc_final: 0.9253 (tmm) REVERT: A 123 MET cc_start: 0.9674 (mmp) cc_final: 0.9393 (mmm) REVERT: A 132 MET cc_start: 0.9412 (tmm) cc_final: 0.9157 (tmm) REVERT: A 257 CYS cc_start: 0.9699 (t) cc_final: 0.9467 (t) REVERT: A 269 MET cc_start: 0.8872 (mtp) cc_final: 0.8475 (mtp) REVERT: A 305 MET cc_start: 0.8792 (mmm) cc_final: 0.8455 (mmm) REVERT: B 44 MET cc_start: 0.4837 (pmm) cc_final: 0.4301 (pmm) REVERT: B 123 MET cc_start: 0.9421 (mmm) cc_final: 0.9118 (mmm) REVERT: B 227 MET cc_start: 0.9089 (mmm) cc_final: 0.8831 (mmm) REVERT: B 269 MET cc_start: 0.9198 (mtp) cc_final: 0.8939 (mtp) REVERT: B 305 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8530 (mmm) REVERT: B 355 MET cc_start: 0.8974 (mtp) cc_final: 0.8341 (mmm) REVERT: C 47 MET cc_start: 0.8076 (ptp) cc_final: 0.7503 (pmm) REVERT: C 82 MET cc_start: 0.8825 (tpt) cc_final: 0.8258 (tpt) REVERT: C 227 MET cc_start: 0.8607 (tpp) cc_final: 0.8316 (mmm) REVERT: C 305 MET cc_start: 0.8162 (mmt) cc_final: 0.7946 (mmm) REVERT: C 313 MET cc_start: 0.9401 (mmm) cc_final: 0.9118 (mmm) REVERT: C 355 MET cc_start: 0.9416 (mtp) cc_final: 0.9212 (mtp) REVERT: D 44 MET cc_start: 0.9129 (mmm) cc_final: 0.8447 (mmm) REVERT: D 47 MET cc_start: 0.6993 (ptm) cc_final: 0.5949 (ppp) REVERT: D 82 MET cc_start: 0.9158 (tpt) cc_final: 0.8782 (tpt) REVERT: D 132 MET cc_start: 0.8679 (ppp) cc_final: 0.8338 (ppp) REVERT: D 227 MET cc_start: 0.9256 (mmm) cc_final: 0.8915 (mmm) REVERT: D 305 MET cc_start: 0.8827 (mmm) cc_final: 0.8526 (mmm) REVERT: D 325 MET cc_start: 0.9151 (mmt) cc_final: 0.8334 (mmm) REVERT: E 82 MET cc_start: 0.9502 (tpt) cc_final: 0.8765 (tpt) REVERT: E 190 MET cc_start: 0.9106 (tmm) cc_final: 0.8836 (tmm) REVERT: E 283 MET cc_start: 0.9278 (mmm) cc_final: 0.8921 (mmm) REVERT: E 299 MET cc_start: 0.8837 (mtm) cc_final: 0.7967 (mmp) REVERT: E 305 MET cc_start: 0.9548 (mmm) cc_final: 0.9291 (mmm) REVERT: E 325 MET cc_start: 0.8432 (mmm) cc_final: 0.8007 (mmm) REVERT: F 82 MET cc_start: 0.9617 (tpt) cc_final: 0.9030 (tpt) REVERT: F 269 MET cc_start: 0.8016 (ttt) cc_final: 0.7750 (ttt) REVERT: H 694 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8910 (tp30) REVERT: H 721 MET cc_start: 0.9164 (mmm) cc_final: 0.8899 (mmm) REVERT: H 812 HIS cc_start: 0.6462 (m90) cc_final: 0.5721 (t70) REVERT: H 913 MET cc_start: 0.4212 (OUTLIER) cc_final: 0.3977 (tpt) REVERT: I 82 MET cc_start: 0.9455 (mmm) cc_final: 0.9187 (mmm) REVERT: I 132 MET cc_start: 0.8522 (tpt) cc_final: 0.8241 (tpp) outliers start: 19 outliers final: 7 residues processed: 143 average time/residue: 0.3412 time to fit residues: 79.7314 Evaluate side-chains 140 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain H residue 913 MET Chi-restraints excluded: chain I residue 176 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 0.6980 chunk 162 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 213 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 0.9980 chunk 257 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24058 Z= 0.216 Angle : 0.630 10.536 32622 Z= 0.301 Chirality : 0.042 0.174 3636 Planarity : 0.004 0.062 4179 Dihedral : 8.959 177.533 3330 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.51 % Allowed : 7.56 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2941 helix: 1.04 (0.14), residues: 1334 sheet: -0.19 (0.24), residues: 469 loop : 0.43 (0.21), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 79 HIS 0.004 0.001 HIS H 703 PHE 0.009 0.001 PHE B 255 TYR 0.016 0.001 TYR B 143 ARG 0.007 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8492 (tpp) cc_final: 0.8060 (tpp) REVERT: A 47 MET cc_start: 0.5561 (ptt) cc_final: 0.5346 (ptt) REVERT: A 82 MET cc_start: 0.9470 (tpt) cc_final: 0.8933 (tpt) REVERT: A 119 MET cc_start: 0.9748 (ttp) cc_final: 0.9192 (tmm) REVERT: A 123 MET cc_start: 0.9636 (mmp) cc_final: 0.9342 (mmm) REVERT: A 132 MET cc_start: 0.9378 (tmm) cc_final: 0.9100 (tmm) REVERT: A 257 CYS cc_start: 0.9690 (t) cc_final: 0.9483 (t) REVERT: A 283 MET cc_start: 0.9347 (mmm) cc_final: 0.9142 (mmm) REVERT: A 299 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8189 (ptp) REVERT: A 305 MET cc_start: 0.8740 (mmm) cc_final: 0.8422 (mmm) REVERT: B 44 MET cc_start: 0.4581 (pmm) cc_final: 0.3865 (pmm) REVERT: B 123 MET cc_start: 0.9338 (mmm) cc_final: 0.9001 (mmm) REVERT: B 227 MET cc_start: 0.9078 (mmm) cc_final: 0.8818 (mmm) REVERT: B 269 MET cc_start: 0.9139 (mtp) cc_final: 0.8889 (mtp) REVERT: B 305 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8588 (mmm) REVERT: B 355 MET cc_start: 0.8967 (mtp) cc_final: 0.8312 (mmm) REVERT: C 82 MET cc_start: 0.8841 (tpt) cc_final: 0.8249 (tpt) REVERT: C 132 MET cc_start: 0.9633 (tmm) cc_final: 0.9408 (tmm) REVERT: C 227 MET cc_start: 0.8574 (tpp) cc_final: 0.8266 (mmm) REVERT: C 305 MET cc_start: 0.8203 (mmt) cc_final: 0.7917 (mmm) REVERT: C 313 MET cc_start: 0.9433 (mmm) cc_final: 0.9155 (mmm) REVERT: C 355 MET cc_start: 0.9407 (mtp) cc_final: 0.9031 (mtp) REVERT: D 44 MET cc_start: 0.9025 (mmm) cc_final: 0.8375 (mmm) REVERT: D 82 MET cc_start: 0.9121 (tpt) cc_final: 0.8781 (tpt) REVERT: D 132 MET cc_start: 0.8598 (ppp) cc_final: 0.8282 (ppp) REVERT: D 227 MET cc_start: 0.9308 (mmm) cc_final: 0.8927 (mmm) REVERT: D 305 MET cc_start: 0.8796 (mmm) cc_final: 0.8484 (mmm) REVERT: D 325 MET cc_start: 0.9140 (mmt) cc_final: 0.8330 (mmm) REVERT: E 82 MET cc_start: 0.9465 (tpt) cc_final: 0.8673 (tpt) REVERT: E 190 MET cc_start: 0.9171 (tmm) cc_final: 0.8882 (tmm) REVERT: E 283 MET cc_start: 0.9314 (mmm) cc_final: 0.8982 (mmm) REVERT: E 299 MET cc_start: 0.8794 (mtm) cc_final: 0.7998 (mmp) REVERT: E 305 MET cc_start: 0.9487 (mmm) cc_final: 0.9183 (mmm) REVERT: E 325 MET cc_start: 0.8410 (mmm) cc_final: 0.7999 (mmm) REVERT: F 82 MET cc_start: 0.9607 (tpt) cc_final: 0.9037 (tpt) REVERT: F 269 MET cc_start: 0.8215 (ttt) cc_final: 0.7944 (ttt) REVERT: F 299 MET cc_start: 0.5311 (ttp) cc_final: 0.4425 (ppp) REVERT: H 694 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8925 (tp30) REVERT: H 721 MET cc_start: 0.9154 (mmm) cc_final: 0.8912 (mmm) REVERT: H 812 HIS cc_start: 0.6178 (m90) cc_final: 0.5452 (t-170) REVERT: H 913 MET cc_start: 0.4178 (OUTLIER) cc_final: 0.3948 (tpt) REVERT: I 44 MET cc_start: 0.2298 (mpt) cc_final: 0.1969 (mpt) REVERT: I 82 MET cc_start: 0.9450 (mmm) cc_final: 0.9180 (mmm) outliers start: 13 outliers final: 7 residues processed: 141 average time/residue: 0.3438 time to fit residues: 79.4988 Evaluate side-chains 142 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain H residue 913 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 287 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 HIS C 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24058 Z= 0.149 Angle : 0.595 9.241 32622 Z= 0.279 Chirality : 0.041 0.179 3636 Planarity : 0.003 0.062 4179 Dihedral : 8.612 170.798 3330 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.59 % Allowed : 8.23 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.16), residues: 2941 helix: 1.29 (0.15), residues: 1334 sheet: -0.08 (0.24), residues: 469 loop : 0.54 (0.21), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 79 HIS 0.004 0.001 HIS H 703 PHE 0.008 0.001 PHE A 255 TYR 0.013 0.001 TYR B 143 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8450 (tpp) cc_final: 0.7917 (tpp) REVERT: A 47 MET cc_start: 0.5480 (ptt) cc_final: 0.5088 (ptt) REVERT: A 82 MET cc_start: 0.9462 (tpt) cc_final: 0.8928 (tpt) REVERT: A 119 MET cc_start: 0.9744 (ttp) cc_final: 0.9115 (tmm) REVERT: A 123 MET cc_start: 0.9608 (mmp) cc_final: 0.9236 (mmm) REVERT: A 132 MET cc_start: 0.9339 (tmm) cc_final: 0.8991 (tmm) REVERT: A 299 MET cc_start: 0.8753 (mtm) cc_final: 0.8181 (ptp) REVERT: A 305 MET cc_start: 0.8765 (mmm) cc_final: 0.8432 (mmm) REVERT: A 325 MET cc_start: 0.8872 (mmm) cc_final: 0.8367 (mmm) REVERT: B 44 MET cc_start: 0.4783 (pmm) cc_final: 0.4110 (pmm) REVERT: B 82 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8646 (mtt) REVERT: B 123 MET cc_start: 0.9287 (mmm) cc_final: 0.8918 (mmm) REVERT: B 227 MET cc_start: 0.9065 (mmm) cc_final: 0.8751 (mmm) REVERT: B 305 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8537 (mmm) REVERT: B 355 MET cc_start: 0.8926 (mtp) cc_final: 0.8250 (mmm) REVERT: C 82 MET cc_start: 0.8830 (tpt) cc_final: 0.8198 (tpt) REVERT: C 132 MET cc_start: 0.9618 (tmm) cc_final: 0.9344 (tmm) REVERT: C 176 MET cc_start: 0.8962 (mmm) cc_final: 0.8464 (mmt) REVERT: C 227 MET cc_start: 0.8542 (tpp) cc_final: 0.8201 (mmm) REVERT: C 305 MET cc_start: 0.8312 (mmt) cc_final: 0.8021 (mmm) REVERT: C 313 MET cc_start: 0.9451 (mmm) cc_final: 0.9179 (mmm) REVERT: C 325 MET cc_start: 0.8522 (mmm) cc_final: 0.8097 (tmm) REVERT: C 355 MET cc_start: 0.9463 (mtp) cc_final: 0.9252 (mtp) REVERT: D 44 MET cc_start: 0.9180 (mmm) cc_final: 0.8790 (mmm) REVERT: D 47 MET cc_start: 0.6856 (ptm) cc_final: 0.6226 (pmm) REVERT: D 82 MET cc_start: 0.9035 (tpt) cc_final: 0.8689 (tpt) REVERT: D 132 MET cc_start: 0.8563 (ppp) cc_final: 0.8284 (ppp) REVERT: D 227 MET cc_start: 0.9396 (mmm) cc_final: 0.9047 (mmm) REVERT: D 305 MET cc_start: 0.8817 (mmm) cc_final: 0.8530 (mmm) REVERT: D 325 MET cc_start: 0.9102 (mmt) cc_final: 0.8352 (mmm) REVERT: E 82 MET cc_start: 0.9427 (tpt) cc_final: 0.8667 (tpp) REVERT: E 176 MET cc_start: 0.8377 (ptp) cc_final: 0.8100 (pmm) REVERT: E 190 MET cc_start: 0.9147 (tmm) cc_final: 0.8817 (tmm) REVERT: E 299 MET cc_start: 0.8712 (mtm) cc_final: 0.8066 (mmp) REVERT: E 305 MET cc_start: 0.9562 (mmm) cc_final: 0.9283 (mmm) REVERT: E 325 MET cc_start: 0.8393 (mmm) cc_final: 0.7994 (mmm) REVERT: F 82 MET cc_start: 0.9587 (tpt) cc_final: 0.9025 (tpt) REVERT: F 269 MET cc_start: 0.8204 (ttt) cc_final: 0.7933 (ttt) REVERT: F 299 MET cc_start: 0.5820 (ttp) cc_final: 0.4849 (ppp) REVERT: F 355 MET cc_start: 0.8404 (mpp) cc_final: 0.8199 (pmm) REVERT: H 694 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8924 (tp30) REVERT: H 721 MET cc_start: 0.9136 (mmm) cc_final: 0.8872 (mmm) REVERT: H 812 HIS cc_start: 0.6178 (m90) cc_final: 0.5432 (t-170) REVERT: H 913 MET cc_start: 0.4084 (OUTLIER) cc_final: 0.3828 (tpt) REVERT: I 44 MET cc_start: 0.2414 (mpt) cc_final: 0.1954 (mpt) REVERT: I 82 MET cc_start: 0.9448 (mmm) cc_final: 0.9178 (mmm) REVERT: I 113 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8191 (mmtm) REVERT: I 132 MET cc_start: 0.8304 (tpp) cc_final: 0.7774 (tpp) outliers start: 15 outliers final: 6 residues processed: 146 average time/residue: 0.3554 time to fit residues: 84.7913 Evaluate side-chains 143 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain H residue 913 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 0.0980 chunk 286 optimal weight: 0.0370 chunk 179 optimal weight: 8.9990 chunk 174 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN F 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24058 Z= 0.136 Angle : 0.598 9.713 32622 Z= 0.278 Chirality : 0.042 0.169 3636 Planarity : 0.003 0.059 4179 Dihedral : 8.327 161.296 3330 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.51 % Allowed : 8.54 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.16), residues: 2941 helix: 1.37 (0.15), residues: 1341 sheet: 0.14 (0.25), residues: 455 loop : 0.60 (0.20), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS H 703 PHE 0.007 0.001 PHE H 920 TYR 0.010 0.001 TYR B 143 ARG 0.008 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8426 (tpp) cc_final: 0.8122 (tpp) REVERT: A 82 MET cc_start: 0.9468 (tpt) cc_final: 0.8962 (tpt) REVERT: A 119 MET cc_start: 0.9749 (ttp) cc_final: 0.9068 (tmm) REVERT: A 123 MET cc_start: 0.9581 (mmp) cc_final: 0.9154 (mmm) REVERT: A 132 MET cc_start: 0.9300 (tmm) cc_final: 0.8855 (tpt) REVERT: A 269 MET cc_start: 0.8967 (mtp) cc_final: 0.8734 (mtp) REVERT: A 299 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8274 (ptp) REVERT: A 305 MET cc_start: 0.8765 (mmm) cc_final: 0.8445 (mmm) REVERT: A 355 MET cc_start: 0.9240 (mmm) cc_final: 0.8639 (tpp) REVERT: B 44 MET cc_start: 0.5067 (pmm) cc_final: 0.4338 (pmm) REVERT: B 82 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8627 (mtt) REVERT: B 123 MET cc_start: 0.9245 (mmm) cc_final: 0.8854 (mmm) REVERT: B 227 MET cc_start: 0.9058 (mmm) cc_final: 0.8739 (mmm) REVERT: B 305 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: B 355 MET cc_start: 0.8914 (mtp) cc_final: 0.8261 (tpp) REVERT: C 82 MET cc_start: 0.8830 (tpt) cc_final: 0.8190 (tpt) REVERT: C 132 MET cc_start: 0.9593 (tmm) cc_final: 0.9312 (tmm) REVERT: C 176 MET cc_start: 0.9026 (mmm) cc_final: 0.8469 (mmt) REVERT: C 190 MET cc_start: 0.9006 (tpp) cc_final: 0.8678 (tpt) REVERT: C 227 MET cc_start: 0.8498 (tpp) cc_final: 0.8150 (mmm) REVERT: C 305 MET cc_start: 0.8416 (mmt) cc_final: 0.8128 (mmm) REVERT: C 313 MET cc_start: 0.9449 (mmm) cc_final: 0.9173 (mmm) REVERT: C 325 MET cc_start: 0.8417 (mmm) cc_final: 0.8071 (tmm) REVERT: C 355 MET cc_start: 0.9478 (mtp) cc_final: 0.9242 (mtp) REVERT: D 44 MET cc_start: 0.9139 (mmm) cc_final: 0.8507 (mmm) REVERT: D 47 MET cc_start: 0.6923 (ptm) cc_final: 0.6033 (ppp) REVERT: D 82 MET cc_start: 0.9006 (tpt) cc_final: 0.8697 (tpt) REVERT: D 227 MET cc_start: 0.9420 (mmm) cc_final: 0.9161 (mmm) REVERT: D 305 MET cc_start: 0.8801 (mmm) cc_final: 0.8481 (mmm) REVERT: D 325 MET cc_start: 0.9085 (mmt) cc_final: 0.8356 (mmm) REVERT: E 82 MET cc_start: 0.9386 (tpt) cc_final: 0.8639 (tpp) REVERT: E 190 MET cc_start: 0.9147 (tmm) cc_final: 0.8796 (tmm) REVERT: E 283 MET cc_start: 0.9277 (mmm) cc_final: 0.8755 (mmm) REVERT: E 299 MET cc_start: 0.8735 (mtm) cc_final: 0.8083 (mmp) REVERT: E 305 MET cc_start: 0.9543 (mmm) cc_final: 0.9273 (mmm) REVERT: E 325 MET cc_start: 0.8474 (mmm) cc_final: 0.8025 (mmm) REVERT: F 82 MET cc_start: 0.9576 (tpt) cc_final: 0.9022 (tpt) REVERT: F 190 MET cc_start: 0.9049 (mmt) cc_final: 0.8826 (mmm) REVERT: F 269 MET cc_start: 0.8163 (ttt) cc_final: 0.7830 (ttt) REVERT: F 299 MET cc_start: 0.5886 (ttp) cc_final: 0.5196 (tmm) REVERT: H 694 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8925 (tp30) REVERT: H 721 MET cc_start: 0.9115 (mmm) cc_final: 0.8850 (mmm) REVERT: I 44 MET cc_start: 0.2571 (mpt) cc_final: 0.2042 (mpt) REVERT: I 113 LYS cc_start: 0.8377 (mmtm) cc_final: 0.8090 (mmtm) REVERT: I 132 MET cc_start: 0.8590 (tpp) cc_final: 0.8293 (tpp) REVERT: I 305 MET cc_start: 0.6912 (mmt) cc_final: 0.6699 (mmt) outliers start: 13 outliers final: 5 residues processed: 145 average time/residue: 0.3241 time to fit residues: 77.5377 Evaluate side-chains 142 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 9.9990 chunk 114 optimal weight: 0.0040 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 20.0000 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN H 812 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24058 Z= 0.150 Angle : 0.613 13.064 32622 Z= 0.285 Chirality : 0.042 0.208 3636 Planarity : 0.003 0.066 4179 Dihedral : 8.176 157.845 3330 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.47 % Allowed : 8.82 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 2941 helix: 1.41 (0.15), residues: 1341 sheet: 0.20 (0.25), residues: 455 loop : 0.63 (0.21), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 79 HIS 0.004 0.001 HIS H 812 PHE 0.007 0.001 PHE H 920 TYR 0.010 0.001 TYR B 143 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8457 (tpp) cc_final: 0.8183 (tpp) REVERT: A 82 MET cc_start: 0.9468 (tpt) cc_final: 0.8973 (tpt) REVERT: A 119 MET cc_start: 0.9750 (ttp) cc_final: 0.9217 (tmm) REVERT: A 123 MET cc_start: 0.9605 (mmp) cc_final: 0.9317 (mmm) REVERT: A 132 MET cc_start: 0.9308 (tmm) cc_final: 0.8977 (tmm) REVERT: A 227 MET cc_start: 0.9353 (ppp) cc_final: 0.9107 (ppp) REVERT: A 269 MET cc_start: 0.8968 (mtp) cc_final: 0.8718 (mtp) REVERT: A 299 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8289 (ptp) REVERT: A 305 MET cc_start: 0.8791 (mmm) cc_final: 0.8473 (mmm) REVERT: A 355 MET cc_start: 0.9232 (mmm) cc_final: 0.8660 (tpp) REVERT: B 44 MET cc_start: 0.4866 (pmm) cc_final: 0.4136 (pmm) REVERT: B 123 MET cc_start: 0.9288 (mmm) cc_final: 0.8856 (mmm) REVERT: B 176 MET cc_start: 0.8977 (mmm) cc_final: 0.8660 (mmm) REVERT: B 227 MET cc_start: 0.9051 (mmm) cc_final: 0.8740 (mmm) REVERT: B 305 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8540 (mmm) REVERT: B 355 MET cc_start: 0.8923 (mtp) cc_final: 0.8277 (tpp) REVERT: C 82 MET cc_start: 0.8836 (tpt) cc_final: 0.8186 (tpt) REVERT: C 132 MET cc_start: 0.9598 (tmm) cc_final: 0.9311 (tmm) REVERT: C 176 MET cc_start: 0.9031 (mmm) cc_final: 0.8384 (mmt) REVERT: C 227 MET cc_start: 0.8499 (tpp) cc_final: 0.8190 (mmm) REVERT: C 305 MET cc_start: 0.8494 (mmt) cc_final: 0.8208 (mmm) REVERT: C 313 MET cc_start: 0.9445 (mmm) cc_final: 0.9170 (mmm) REVERT: C 325 MET cc_start: 0.8387 (mmm) cc_final: 0.8147 (tmm) REVERT: C 355 MET cc_start: 0.9482 (mtp) cc_final: 0.9251 (mtp) REVERT: D 44 MET cc_start: 0.9143 (mmm) cc_final: 0.8459 (mmm) REVERT: D 47 MET cc_start: 0.7032 (ptm) cc_final: 0.6089 (ppp) REVERT: D 82 MET cc_start: 0.9031 (tpt) cc_final: 0.8711 (tpt) REVERT: D 132 MET cc_start: 0.8562 (ppp) cc_final: 0.8291 (ppp) REVERT: D 227 MET cc_start: 0.9421 (mmm) cc_final: 0.9208 (mmm) REVERT: D 305 MET cc_start: 0.8823 (mmm) cc_final: 0.8501 (mmm) REVERT: D 325 MET cc_start: 0.9044 (mmt) cc_final: 0.8307 (mmm) REVERT: E 82 MET cc_start: 0.9363 (tpt) cc_final: 0.8584 (tpt) REVERT: E 176 MET cc_start: 0.8583 (ptp) cc_final: 0.8159 (pmm) REVERT: E 190 MET cc_start: 0.9170 (tmm) cc_final: 0.8801 (tmm) REVERT: E 283 MET cc_start: 0.9253 (mmm) cc_final: 0.8892 (mmm) REVERT: E 299 MET cc_start: 0.8739 (mtm) cc_final: 0.8102 (mmp) REVERT: E 305 MET cc_start: 0.9527 (mmm) cc_final: 0.9272 (mmm) REVERT: E 325 MET cc_start: 0.8511 (mmm) cc_final: 0.8025 (mmm) REVERT: E 355 MET cc_start: 0.9252 (mtp) cc_final: 0.8993 (mtt) REVERT: F 82 MET cc_start: 0.9589 (tpt) cc_final: 0.9023 (tpt) REVERT: F 176 MET cc_start: 0.7240 (ptp) cc_final: 0.6986 (pmm) REVERT: F 269 MET cc_start: 0.8173 (ttt) cc_final: 0.7839 (ttt) REVERT: F 299 MET cc_start: 0.5947 (ttp) cc_final: 0.5257 (tmm) REVERT: H 694 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8932 (tp30) REVERT: H 721 MET cc_start: 0.9124 (mmm) cc_final: 0.8858 (mmm) REVERT: I 44 MET cc_start: 0.2719 (mpt) cc_final: 0.2382 (mpt) REVERT: I 82 MET cc_start: 0.9071 (mmm) cc_final: 0.8771 (mmm) REVERT: I 113 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8095 (mmtm) REVERT: I 132 MET cc_start: 0.8633 (tpp) cc_final: 0.8072 (tpp) outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 0.3278 time to fit residues: 76.6880 Evaluate side-chains 142 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 30.0000 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 160 optimal weight: 0.0980 chunk 116 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN B 111 ASN B 173 HIS C 12 ASN C 280 ASN D 263 GLN E 297 ASN H 640 ASN I 41 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24058 Z= 0.295 Angle : 0.722 12.883 32622 Z= 0.349 Chirality : 0.043 0.189 3636 Planarity : 0.004 0.067 4179 Dihedral : 8.315 158.775 3330 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.47 % Allowed : 9.10 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.16), residues: 2941 helix: 1.10 (0.14), residues: 1328 sheet: -0.12 (0.24), residues: 490 loop : 0.65 (0.21), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 86 HIS 0.009 0.001 HIS D 173 PHE 0.016 0.002 PHE E 200 TYR 0.016 0.002 TYR B 69 ARG 0.007 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8475 (tpp) cc_final: 0.8211 (tpp) REVERT: A 82 MET cc_start: 0.9491 (tpt) cc_final: 0.8990 (tpt) REVERT: A 119 MET cc_start: 0.9764 (ttp) cc_final: 0.9229 (tmm) REVERT: A 123 MET cc_start: 0.9687 (mmp) cc_final: 0.9353 (mmm) REVERT: A 132 MET cc_start: 0.9391 (tmm) cc_final: 0.9144 (tmm) REVERT: A 299 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8411 (ptp) REVERT: A 305 MET cc_start: 0.8766 (mmm) cc_final: 0.8461 (mmm) REVERT: B 123 MET cc_start: 0.9434 (mmm) cc_final: 0.9058 (mmm) REVERT: B 227 MET cc_start: 0.9030 (mmm) cc_final: 0.8785 (mmm) REVERT: B 305 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8631 (mmm) REVERT: B 355 MET cc_start: 0.8954 (mtp) cc_final: 0.8251 (tmm) REVERT: C 82 MET cc_start: 0.8895 (tpt) cc_final: 0.8490 (tpt) REVERT: C 190 MET cc_start: 0.9024 (tpp) cc_final: 0.8726 (tpt) REVERT: C 227 MET cc_start: 0.8728 (tpp) cc_final: 0.8383 (mmm) REVERT: C 305 MET cc_start: 0.8347 (mmt) cc_final: 0.8118 (mmm) REVERT: C 313 MET cc_start: 0.9445 (mmm) cc_final: 0.9151 (mmm) REVERT: C 325 MET cc_start: 0.8276 (mmm) cc_final: 0.8038 (tmm) REVERT: D 44 MET cc_start: 0.9098 (mmm) cc_final: 0.8518 (mmm) REVERT: D 47 MET cc_start: 0.7308 (ptm) cc_final: 0.6384 (ppp) REVERT: D 82 MET cc_start: 0.9146 (tpt) cc_final: 0.8763 (tpt) REVERT: D 132 MET cc_start: 0.8723 (ppp) cc_final: 0.8407 (ppp) REVERT: D 227 MET cc_start: 0.9420 (mmm) cc_final: 0.9201 (mmm) REVERT: D 305 MET cc_start: 0.8818 (mmm) cc_final: 0.8520 (mmm) REVERT: D 325 MET cc_start: 0.9103 (mmt) cc_final: 0.8238 (mmm) REVERT: E 82 MET cc_start: 0.9478 (tpt) cc_final: 0.8742 (tpt) REVERT: E 176 MET cc_start: 0.8391 (ptp) cc_final: 0.8162 (pmm) REVERT: E 190 MET cc_start: 0.9287 (tmm) cc_final: 0.8953 (tmm) REVERT: E 283 MET cc_start: 0.9270 (mmm) cc_final: 0.8899 (mmm) REVERT: E 299 MET cc_start: 0.8763 (mtm) cc_final: 0.8030 (mmp) REVERT: E 305 MET cc_start: 0.9481 (mmm) cc_final: 0.9184 (mmm) REVERT: E 325 MET cc_start: 0.8426 (mmm) cc_final: 0.8047 (mmm) REVERT: F 176 MET cc_start: 0.7323 (ptp) cc_final: 0.7101 (pmm) REVERT: F 299 MET cc_start: 0.6197 (ttp) cc_final: 0.5347 (ppp) REVERT: H 694 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8998 (tp30) REVERT: H 721 MET cc_start: 0.9158 (mmm) cc_final: 0.8882 (mmm) REVERT: I 44 MET cc_start: 0.3815 (mpt) cc_final: 0.2931 (mpt) REVERT: I 82 MET cc_start: 0.9118 (mmm) cc_final: 0.8814 (mmm) REVERT: I 123 MET cc_start: 0.6880 (tmm) cc_final: 0.6432 (tmm) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 0.3276 time to fit residues: 75.0674 Evaluate side-chains 138 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 1.9990 chunk 282 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24058 Z= 0.312 Angle : 0.748 11.460 32622 Z= 0.362 Chirality : 0.044 0.238 3636 Planarity : 0.004 0.064 4179 Dihedral : 8.236 150.068 3330 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.44 % Allowed : 9.57 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2941 helix: 0.86 (0.14), residues: 1321 sheet: -0.38 (0.24), residues: 504 loop : 0.46 (0.21), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 86 HIS 0.007 0.001 HIS D 173 PHE 0.012 0.002 PHE E 200 TYR 0.015 0.002 TYR I 133 ARG 0.006 0.001 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5882 Ramachandran restraints generated. 2941 Oldfield, 0 Emsley, 2941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8553 (tpp) cc_final: 0.7980 (tpp) REVERT: A 47 MET cc_start: 0.5044 (ptt) cc_final: 0.4677 (ptp) REVERT: A 82 MET cc_start: 0.9516 (tpt) cc_final: 0.8994 (tpt) REVERT: A 119 MET cc_start: 0.9767 (ttp) cc_final: 0.9243 (tmm) REVERT: A 123 MET cc_start: 0.9681 (mmp) cc_final: 0.9339 (mmm) REVERT: A 132 MET cc_start: 0.9363 (tmm) cc_final: 0.9095 (tmm) REVERT: A 227 MET cc_start: 0.9222 (ppp) cc_final: 0.8995 (ppp) REVERT: A 299 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8429 (ptp) REVERT: B 123 MET cc_start: 0.9474 (mmm) cc_final: 0.9089 (mmm) REVERT: B 227 MET cc_start: 0.9035 (mmm) cc_final: 0.8785 (mmm) REVERT: B 305 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8629 (mmm) REVERT: B 355 MET cc_start: 0.8935 (mtp) cc_final: 0.8245 (tmm) REVERT: C 82 MET cc_start: 0.8914 (tpt) cc_final: 0.8498 (tpt) REVERT: C 190 MET cc_start: 0.9053 (tpp) cc_final: 0.8748 (tpt) REVERT: C 227 MET cc_start: 0.8801 (tpp) cc_final: 0.8436 (mmm) REVERT: C 305 MET cc_start: 0.8348 (mmt) cc_final: 0.8137 (mmm) REVERT: C 313 MET cc_start: 0.9450 (mmm) cc_final: 0.9157 (mmm) REVERT: C 355 MET cc_start: 0.9390 (mtp) cc_final: 0.9153 (mtp) REVERT: D 44 MET cc_start: 0.9140 (mmm) cc_final: 0.8607 (mmm) REVERT: D 47 MET cc_start: 0.7278 (ptm) cc_final: 0.6251 (ppp) REVERT: D 82 MET cc_start: 0.9164 (tpt) cc_final: 0.8771 (tpt) REVERT: D 132 MET cc_start: 0.8720 (ppp) cc_final: 0.8455 (ppp) REVERT: D 227 MET cc_start: 0.9413 (mmm) cc_final: 0.9177 (mmm) REVERT: D 283 MET cc_start: 0.9101 (mmm) cc_final: 0.8812 (mmm) REVERT: D 299 MET cc_start: 0.8051 (mpp) cc_final: 0.7509 (mpp) REVERT: D 305 MET cc_start: 0.8716 (mmm) cc_final: 0.8384 (mmm) REVERT: D 325 MET cc_start: 0.9181 (mmt) cc_final: 0.8192 (mmm) REVERT: E 82 MET cc_start: 0.9453 (tpt) cc_final: 0.8712 (tpt) REVERT: E 176 MET cc_start: 0.8421 (ptp) cc_final: 0.8191 (pmm) REVERT: E 190 MET cc_start: 0.9374 (tmm) cc_final: 0.9162 (tmm) REVERT: E 283 MET cc_start: 0.9255 (mmm) cc_final: 0.8882 (mmm) REVERT: E 299 MET cc_start: 0.8879 (mtm) cc_final: 0.8146 (mmt) REVERT: E 305 MET cc_start: 0.9517 (mmm) cc_final: 0.9282 (mmm) REVERT: E 325 MET cc_start: 0.8443 (mmm) cc_final: 0.8125 (mmm) REVERT: F 47 MET cc_start: 0.7541 (pmm) cc_final: 0.7230 (pmm) REVERT: F 180 LEU cc_start: 0.9704 (tt) cc_final: 0.9274 (pp) REVERT: F 269 MET cc_start: 0.8637 (ttt) cc_final: 0.8155 (ppp) REVERT: F 299 MET cc_start: 0.6342 (ttp) cc_final: 0.5583 (ppp) REVERT: H 721 MET cc_start: 0.9106 (mmm) cc_final: 0.8800 (mmm) REVERT: I 44 MET cc_start: 0.4938 (mpt) cc_final: 0.3747 (mpt) REVERT: I 82 MET cc_start: 0.9067 (mmm) cc_final: 0.8751 (mmm) REVERT: I 123 MET cc_start: 0.7493 (tmm) cc_final: 0.7062 (tmm) outliers start: 11 outliers final: 6 residues processed: 138 average time/residue: 0.3367 time to fit residues: 76.5260 Evaluate side-chains 139 residues out of total 2528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain B residue 10 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN I 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.033879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.022747 restraints weight = 285844.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.023142 restraints weight = 183566.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.023468 restraints weight = 134188.609| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24058 Z= 0.335 Angle : 0.779 11.223 32622 Z= 0.377 Chirality : 0.044 0.221 3636 Planarity : 0.004 0.064 4179 Dihedral : 8.231 149.851 3330 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.55 % Allowed : 9.65 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2941 helix: 0.72 (0.14), residues: 1319 sheet: -0.52 (0.24), residues: 504 loop : 0.32 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 86 HIS 0.007 0.002 HIS D 173 PHE 0.016 0.002 PHE E 200 TYR 0.017 0.002 TYR I 337 ARG 0.007 0.001 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3732.88 seconds wall clock time: 69 minutes 45.51 seconds (4185.51 seconds total)