Starting phenix.real_space_refine on Wed Jun 18 19:38:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8voa_43369/06_2025/8voa_43369_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8voa_43369/06_2025/8voa_43369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8voa_43369/06_2025/8voa_43369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8voa_43369/06_2025/8voa_43369.map" model { file = "/net/cci-nas-00/data/ceres_data/8voa_43369/06_2025/8voa_43369_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8voa_43369/06_2025/8voa_43369_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 140 5.16 5 C 13504 2.51 5 N 3654 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21459 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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: 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: "G" 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: 14.35, per 1000 atoms: 0.67 Number of scatterers: 21459 At special positions: 0 Unit cell: (214.24, 105.06, 156.56, 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 140 16.00 P 12 15.00 Mg 6 11.99 O 4143 8.00 N 3654 7.00 C 13504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.8 seconds 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 57 sheets defined 41.4% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.518A pdb=" N LEU A 119 " --> pdb=" O GLU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 371 through 375 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 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.968A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 146 removed outlier: 3.868A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 4.080A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.516A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.798A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.955A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.087A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 3.804A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.427A pdb=" N ARG C 62 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY C 63 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.603A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.882A 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 172 through 175 removed outlier: 3.760A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.666A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.897A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.006A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.722A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.817A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.877A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.880A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.747A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.976A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 removed outlier: 4.026A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.253A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.804A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.885A 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 removed outlier: 3.597A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 removed outlier: 4.044A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.649A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 273 through 283 removed outlier: 3.827A pdb=" N MET E 283 " --> pdb=" O TYR E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.894A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.588A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.892A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.516A pdb=" N TYR E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.121A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.545A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.654A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.814A 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: 3.811A 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 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.670A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.850A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 4.023A pdb=" N MET F 305 " --> pdb=" O GLY F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 353 removed outlier: 3.691A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 350 through 353' Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 373 removed outlier: 4.308A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.579A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.584A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 252 through 260 removed outlier: 4.181A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 296 removed outlier: 3.999A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 349 through 356 removed outlier: 4.142A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 5.559A pdb=" N TYR A 23 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 36 " --> pdb=" O TYR A 23 " (cutoff:3.500A) 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 91 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.839A pdb=" N ALA A 123 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A 113 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N CYS A 121 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 185 through 189 removed outlier: 3.619A pdb=" N SER A 187 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.626A pdb=" N ARG A 167 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS A 154 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL A 165 " --> pdb=" O HIS A 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 217 removed outlier: 3.511A pdb=" N ALA A 222 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 217 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AB2, first strand: chain 'A' and resid 345 through 348 removed outlier: 3.500A pdb=" N THR A 346 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.745A pdb=" N SER A 274 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA A 283 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 316 through 317 Processing sheet with id=AB5, first strand: chain 'A' and resid 354 through 357 removed outlier: 6.777A pdb=" N PHE A 354 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER A 366 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.656A pdb=" N ARG A 408 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLY A 396 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA A 406 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 414 through 419 Processing sheet with id=AB8, first strand: chain 'A' and resid 432 through 434 removed outlier: 5.629A pdb=" N TYR A 432 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 444 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.553A pdb=" N CYS A 456 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) removed outlier: 13.062A pdb=" N VAL A 461 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 9.352A pdb=" N GLY A 472 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LYS A 471 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA A 480 " --> pdb=" O LYS A 471 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP A 473 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU A 478 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 452 through 457 removed outlier: 3.553A pdb=" N CYS A 456 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 460 " --> pdb=" O CYS A 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.919A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 357 " --> pdb=" O MET B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.834A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.834A pdb=" N GLN B 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 166 " --> pdb=" O TYR C 169 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.611A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.628A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.436A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AD9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AE2, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.898A pdb=" N VAL D 152 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE D 165 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AE4, first strand: chain 'E' and resid 8 through 9 removed outlier: 6.158A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 135 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AE6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AE7, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.336A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 162 " --> pdb=" O MET F 176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.336A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS F 161 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 152 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.741A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.516A pdb=" N VAL E 298 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AF4, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.638A pdb=" N ALA F 29 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AF6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AF8, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.792A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU G 107 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET G 132 " --> pdb=" O ILE G 357 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AG1, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AG2, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.969A pdb=" N VAL G 298 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 238 through 241 913 hydrogen bonds defined for protein. 2355 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: 9.46 Time building geometry restraints manager: 6.03 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: 4614 1.33 - 1.45: 4910 1.45 - 1.57: 12143 1.57 - 1.69: 18 1.69 - 1.81: 239 Bond restraints: 21924 Sorted by residual: bond pdb=" N ILE G 75 " pdb=" CA ILE G 75 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.22e-02 6.72e+03 9.34e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.59e+00 bond pdb=" N MET E 355 " pdb=" CA MET E 355 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.48e+00 bond pdb=" N ILE G 76 " pdb=" CA ILE G 76 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.27e+00 bond pdb=" N ILE A 395 " pdb=" CA ILE A 395 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.17e-02 7.31e+03 8.20e+00 ... (remaining 21919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 28730 1.41 - 2.82: 740 2.82 - 4.23: 197 4.23 - 5.64: 60 5.64 - 7.05: 12 Bond angle restraints: 29739 Sorted by residual: angle pdb=" C LYS A 399 " pdb=" CA LYS A 399 " pdb=" CB LYS A 399 " ideal model delta sigma weight residual 116.54 111.57 4.97 1.15e+00 7.56e-01 1.87e+01 angle pdb=" CA GLY A 393 " pdb=" C GLY A 393 " pdb=" O GLY A 393 " ideal model delta sigma weight residual 121.04 118.00 3.04 7.90e-01 1.60e+00 1.48e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 113.07 107.94 5.13 1.37e+00 5.33e-01 1.40e+01 angle pdb=" N GLU E 205 " pdb=" CA GLU E 205 " pdb=" C GLU E 205 " ideal model delta sigma weight residual 112.54 108.08 4.46 1.22e+00 6.72e-01 1.34e+01 angle pdb=" CA PHE A 394 " pdb=" CB PHE A 394 " pdb=" CG PHE A 394 " ideal model delta sigma weight residual 113.80 117.31 -3.51 1.00e+00 1.00e+00 1.23e+01 ... (remaining 29734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 12113 22.19 - 44.37: 925 44.37 - 66.56: 89 66.56 - 88.74: 26 88.74 - 110.93: 7 Dihedral angle restraints: 13160 sinusoidal: 5298 harmonic: 7862 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 -170.93 110.93 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -169.63 109.63 1 2.00e+01 2.50e-03 3.21e+01 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 -168.84 108.84 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 13157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2668 0.056 - 0.113: 549 0.113 - 0.169: 56 0.169 - 0.225: 6 0.225 - 0.282: 2 Chirality restraints: 3281 Sorted by residual: chirality pdb=" CA PHE A 394 " pdb=" N PHE A 394 " pdb=" C PHE A 394 " pdb=" CB PHE A 394 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA GLU E 205 " pdb=" N GLU E 205 " pdb=" C GLU E 205 " pdb=" CB GLU E 205 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE G 71 " pdb=" N ILE G 71 " pdb=" C ILE G 71 " pdb=" CB ILE G 71 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3278 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 101 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO E 102 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 102 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 102 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 393 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C GLY A 393 " -0.028 2.00e-02 2.50e+03 pdb=" O GLY A 393 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 394 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 204 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C ALA E 204 " -0.027 2.00e-02 2.50e+03 pdb=" O ALA E 204 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU E 205 " 0.009 2.00e-02 2.50e+03 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 225 2.52 - 3.12: 16481 3.12 - 3.71: 34165 3.71 - 4.31: 46884 4.31 - 4.90: 78587 Nonbonded interactions: 176342 Sorted by model distance: nonbonded pdb=" CE MET F 132 " pdb=" N TYR F 133 " model vdw 1.925 3.540 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 1.993 2.170 nonbonded pdb=" O2A ADP F 401 " pdb="MG MG F 402 " model vdw 2.096 2.170 nonbonded pdb=" O2A ADP D 401 " pdb="MG MG D 402 " model vdw 2.103 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.120 2.170 ... (remaining 176337 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 10.730 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: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 52.360 Find NCS groups from input model: 0.670 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: 0.010 Load rotamer database and sin/cos tables:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21924 Z= 0.194 Angle : 0.612 7.047 29739 Z= 0.320 Chirality : 0.046 0.282 3281 Planarity : 0.004 0.076 3827 Dihedral : 14.998 110.928 8126 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.26 % Allowed : 4.19 % Favored : 95.54 % 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: 0.13 (0.17), residues: 2691 helix: 0.37 (0.18), residues: 900 sheet: 0.40 (0.24), residues: 494 loop : -0.11 (0.19), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 79 HIS 0.003 0.001 HIS E 87 PHE 0.017 0.001 PHE A 394 TYR 0.018 0.001 TYR B 279 ARG 0.004 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.21829 ( 896) hydrogen bonds : angle 7.70823 ( 2355) covalent geometry : bond 0.00384 (21924) covalent geometry : angle 0.61214 (29739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 399 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 PHE cc_start: 0.7930 (m-80) cc_final: 0.7516 (m-80) REVERT: A 252 GLU cc_start: 0.8478 (mp0) cc_final: 0.8163 (mp0) REVERT: A 285 GLN cc_start: 0.7749 (mp10) cc_final: 0.7426 (mp10) REVERT: B 119 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8374 (ptp) REVERT: B 153 LEU cc_start: 0.9189 (tp) cc_final: 0.8969 (tp) REVERT: B 191 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7899 (ttmt) REVERT: B 356 TRP cc_start: 0.8149 (m100) cc_final: 0.7246 (m100) REVERT: C 54 VAL cc_start: 0.8911 (t) cc_final: 0.8620 (m) REVERT: C 93 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8102 (tm-30) REVERT: C 121 GLN cc_start: 0.7259 (tm-30) cc_final: 0.6976 (tm-30) REVERT: C 217 CYS cc_start: 0.8442 (m) cc_final: 0.7699 (m) REVERT: D 137 GLN cc_start: 0.7993 (mp10) cc_final: 0.7712 (mp10) REVERT: D 151 ILE cc_start: 0.8518 (mm) cc_final: 0.8264 (mt) REVERT: D 192 ILE cc_start: 0.8345 (tp) cc_final: 0.8061 (tp) REVERT: D 234 SER cc_start: 0.8221 (m) cc_final: 0.7681 (p) REVERT: D 291 LYS cc_start: 0.8009 (tttm) cc_final: 0.7335 (mmtt) REVERT: D 355 MET cc_start: 0.8542 (mtt) cc_final: 0.8217 (mmp) REVERT: D 373 LYS cc_start: 0.8391 (tptm) cc_final: 0.8045 (tptm) REVERT: E 149 THR cc_start: 0.8297 (p) cc_final: 0.8071 (t) REVERT: E 252 ASN cc_start: 0.8290 (p0) cc_final: 0.7942 (p0) REVERT: E 328 LYS cc_start: 0.8297 (pptt) cc_final: 0.7734 (ptmm) REVERT: E 356 TRP cc_start: 0.6258 (m100) cc_final: 0.5885 (m100) REVERT: F 81 ASP cc_start: 0.8777 (m-30) cc_final: 0.8540 (m-30) REVERT: F 149 THR cc_start: 0.8897 (p) cc_final: 0.8688 (p) REVERT: F 217 CYS cc_start: 0.8184 (m) cc_final: 0.7870 (m) REVERT: F 246 GLN cc_start: 0.7945 (mt0) cc_final: 0.7669 (mt0) REVERT: F 289 ILE cc_start: 0.8207 (mm) cc_final: 0.7939 (mt) REVERT: F 299 MET cc_start: 0.8091 (mtm) cc_final: 0.7715 (mtm) REVERT: F 355 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6744 (mpp) REVERT: G 76 ILE cc_start: 0.8356 (mt) cc_final: 0.7934 (mt) REVERT: G 121 GLN cc_start: 0.8375 (tt0) cc_final: 0.7905 (tm-30) REVERT: G 195 GLU cc_start: 0.7889 (tp30) cc_final: 0.7671 (tt0) REVERT: G 222 ASP cc_start: 0.8545 (t0) cc_final: 0.8240 (t0) REVERT: G 237 GLU cc_start: 0.8323 (mp0) cc_final: 0.8057 (mp0) REVERT: G 362 TYR cc_start: 0.7885 (t80) cc_final: 0.7625 (t80) outliers start: 6 outliers final: 1 residues processed: 399 average time/residue: 0.3606 time to fit residues: 221.7252 Evaluate side-chains 285 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 282 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain F residue 355 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 245 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 310 HIS D 111 ASN D 128 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** F 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.108990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.090416 restraints weight = 51226.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.091660 restraints weight = 30634.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092804 restraints weight = 22125.881| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21924 Z= 0.135 Angle : 0.614 7.301 29739 Z= 0.305 Chirality : 0.046 0.185 3281 Planarity : 0.004 0.044 3827 Dihedral : 7.967 100.998 3057 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.57 % Allowed : 9.13 % Favored : 89.30 % 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: 0.30 (0.17), residues: 2691 helix: 0.41 (0.17), residues: 948 sheet: 0.58 (0.25), residues: 488 loop : 0.03 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.011 0.001 HIS A 139 PHE 0.013 0.001 PHE G 223 TYR 0.033 0.001 TYR F 198 ARG 0.004 0.000 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 896) hydrogen bonds : angle 5.78969 ( 2355) covalent geometry : bond 0.00305 (21924) covalent geometry : angle 0.61417 (29739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 2.853 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: A 285 GLN cc_start: 0.7544 (mp10) cc_final: 0.7054 (mp10) REVERT: B 82 MET cc_start: 0.8266 (tpt) cc_final: 0.7943 (tpt) REVERT: B 119 MET cc_start: 0.8545 (ptp) cc_final: 0.8316 (ptp) REVERT: B 198 TYR cc_start: 0.8886 (m-80) cc_final: 0.8604 (m-80) REVERT: B 227 MET cc_start: 0.8197 (mmm) cc_final: 0.7816 (mmm) REVERT: B 356 TRP cc_start: 0.7960 (m100) cc_final: 0.7405 (m100) REVERT: C 54 VAL cc_start: 0.8619 (t) cc_final: 0.8327 (m) REVERT: C 132 MET cc_start: 0.8782 (ptt) cc_final: 0.8566 (ptt) REVERT: C 217 CYS cc_start: 0.7998 (m) cc_final: 0.7377 (m) REVERT: D 192 ILE cc_start: 0.8757 (tp) cc_final: 0.8468 (tp) REVERT: D 234 SER cc_start: 0.8306 (m) cc_final: 0.7643 (p) REVERT: D 291 LYS cc_start: 0.8119 (tttm) cc_final: 0.7749 (mmtt) REVERT: E 265 SER cc_start: 0.8162 (p) cc_final: 0.7876 (t) REVERT: F 149 THR cc_start: 0.8911 (p) cc_final: 0.8657 (p) REVERT: F 257 CYS cc_start: 0.8761 (t) cc_final: 0.8329 (t) REVERT: F 289 ILE cc_start: 0.8496 (mm) cc_final: 0.8114 (mt) REVERT: F 355 MET cc_start: 0.7195 (mpp) cc_final: 0.6726 (mpp) REVERT: G 68 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7766 (tttp) REVERT: G 121 GLN cc_start: 0.8110 (tt0) cc_final: 0.7770 (tm-30) REVERT: G 362 TYR cc_start: 0.7718 (t80) cc_final: 0.7431 (t80) outliers start: 36 outliers final: 24 residues processed: 337 average time/residue: 0.3819 time to fit residues: 211.6479 Evaluate side-chains 282 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 270 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 7 optimal weight: 0.0030 chunk 212 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 245 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086602 restraints weight = 51738.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086795 restraints weight = 33388.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.087945 restraints weight = 27580.551| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21924 Z= 0.234 Angle : 0.685 7.350 29739 Z= 0.342 Chirality : 0.049 0.201 3281 Planarity : 0.004 0.046 3827 Dihedral : 8.227 107.257 3048 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.23 % Allowed : 12.71 % Favored : 85.06 % 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: 0.05 (0.17), residues: 2691 helix: 0.21 (0.17), residues: 960 sheet: 0.35 (0.24), residues: 488 loop : -0.08 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 356 HIS 0.008 0.001 HIS F 101 PHE 0.016 0.002 PHE B 200 TYR 0.017 0.002 TYR F 198 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 896) hydrogen bonds : angle 5.63016 ( 2355) covalent geometry : bond 0.00546 (21924) covalent geometry : angle 0.68484 (29739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.7820 (mp10) cc_final: 0.7179 (mp10) REVERT: B 110 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8703 (tt) REVERT: B 198 TYR cc_start: 0.8926 (m-80) cc_final: 0.8708 (m-80) REVERT: B 286 ASP cc_start: 0.6933 (t0) cc_final: 0.6388 (t0) REVERT: B 352 PHE cc_start: 0.8472 (t80) cc_final: 0.8259 (t80) REVERT: B 356 TRP cc_start: 0.8014 (m100) cc_final: 0.7632 (m100) REVERT: C 54 VAL cc_start: 0.8676 (t) cc_final: 0.8392 (m) REVERT: C 132 MET cc_start: 0.8821 (ptt) cc_final: 0.8594 (ptt) REVERT: D 192 ILE cc_start: 0.8885 (tp) cc_final: 0.8537 (tp) REVERT: D 234 SER cc_start: 0.8372 (m) cc_final: 0.7647 (p) REVERT: D 313 MET cc_start: 0.9040 (tpp) cc_final: 0.8482 (ttm) REVERT: E 92 ASN cc_start: 0.7198 (m-40) cc_final: 0.6988 (t0) REVERT: E 121 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8351 (tm-30) REVERT: E 244 ASP cc_start: 0.7619 (p0) cc_final: 0.7403 (p0) REVERT: E 265 SER cc_start: 0.8189 (p) cc_final: 0.7970 (t) REVERT: F 162 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8385 (m-40) REVERT: F 257 CYS cc_start: 0.8789 (t) cc_final: 0.8390 (t) REVERT: F 289 ILE cc_start: 0.8729 (mm) cc_final: 0.8435 (mt) REVERT: F 355 MET cc_start: 0.7100 (mpp) cc_final: 0.6884 (mpp) REVERT: G 121 GLN cc_start: 0.8034 (tt0) cc_final: 0.7768 (tm-30) REVERT: G 279 TYR cc_start: 0.8624 (t80) cc_final: 0.8018 (t80) REVERT: G 362 TYR cc_start: 0.7887 (t80) cc_final: 0.7552 (t80) REVERT: G 372 ARG cc_start: 0.7182 (mtm110) cc_final: 0.6665 (mtm110) outliers start: 51 outliers final: 39 residues processed: 305 average time/residue: 0.3064 time to fit residues: 149.9676 Evaluate side-chains 278 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 237 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 119 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 278 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 266 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS C 246 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN F 87 HIS ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.088064 restraints weight = 52075.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089700 restraints weight = 34217.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.090490 restraints weight = 23306.863| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21924 Z= 0.129 Angle : 0.598 7.672 29739 Z= 0.293 Chirality : 0.045 0.164 3281 Planarity : 0.004 0.040 3827 Dihedral : 7.907 102.524 3048 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.01 % Allowed : 14.55 % Favored : 83.44 % 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: 0.17 (0.17), residues: 2691 helix: 0.32 (0.17), residues: 960 sheet: 0.41 (0.24), residues: 498 loop : -0.02 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.006 0.001 HIS C 275 PHE 0.010 0.001 PHE F 255 TYR 0.013 0.001 TYR F 198 ARG 0.003 0.000 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 896) hydrogen bonds : angle 5.33686 ( 2355) covalent geometry : bond 0.00298 (21924) covalent geometry : angle 0.59755 (29739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 GLN cc_start: 0.7673 (mp10) cc_final: 0.6968 (mp10) REVERT: B 41 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 82 MET cc_start: 0.8543 (mmm) cc_final: 0.6261 (tmm) REVERT: B 86 TRP cc_start: 0.8353 (OUTLIER) cc_final: 0.7102 (m-10) REVERT: B 286 ASP cc_start: 0.6828 (t0) cc_final: 0.6331 (t0) REVERT: B 356 TRP cc_start: 0.7926 (m100) cc_final: 0.7537 (m100) REVERT: C 54 VAL cc_start: 0.8525 (t) cc_final: 0.8292 (m) REVERT: C 217 CYS cc_start: 0.8184 (m) cc_final: 0.7429 (m) REVERT: D 192 ILE cc_start: 0.8897 (tp) cc_final: 0.8500 (tp) REVERT: D 234 SER cc_start: 0.8360 (m) cc_final: 0.7704 (p) REVERT: D 313 MET cc_start: 0.9037 (tpp) cc_final: 0.8483 (ttm) REVERT: E 14 SER cc_start: 0.7359 (t) cc_final: 0.7076 (m) REVERT: E 121 GLN cc_start: 0.8960 (tm-30) cc_final: 0.8211 (tm-30) REVERT: E 244 ASP cc_start: 0.7708 (p0) cc_final: 0.7458 (p0) REVERT: E 265 SER cc_start: 0.8204 (p) cc_final: 0.7984 (t) REVERT: E 354 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8242 (mp10) REVERT: F 289 ILE cc_start: 0.8714 (mm) cc_final: 0.8409 (mt) REVERT: F 349 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6134 (mp) REVERT: F 355 MET cc_start: 0.7117 (mpp) cc_final: 0.6916 (mpp) REVERT: G 65 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8349 (pp) REVERT: G 68 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7732 (tttt) REVERT: G 103 THR cc_start: 0.9119 (t) cc_final: 0.8841 (t) REVERT: G 121 GLN cc_start: 0.8094 (tt0) cc_final: 0.7800 (tm-30) REVERT: G 283 MET cc_start: 0.8179 (tpp) cc_final: 0.7933 (mpp) REVERT: G 305 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7299 (mpp) REVERT: G 362 TYR cc_start: 0.7933 (t80) cc_final: 0.7577 (t80) outliers start: 46 outliers final: 30 residues processed: 306 average time/residue: 0.3220 time to fit residues: 161.5125 Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 101 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088241 restraints weight = 51830.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.089862 restraints weight = 32952.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090808 restraints weight = 24114.420| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21924 Z= 0.137 Angle : 0.593 7.881 29739 Z= 0.290 Chirality : 0.045 0.161 3281 Planarity : 0.004 0.043 3827 Dihedral : 7.863 102.428 3048 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.66 % Allowed : 15.29 % Favored : 82.04 % 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: 0.20 (0.17), residues: 2691 helix: 0.36 (0.17), residues: 960 sheet: 0.40 (0.24), residues: 498 loop : -0.01 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 356 HIS 0.006 0.001 HIS F 101 PHE 0.010 0.001 PHE G 262 TYR 0.012 0.001 TYR F 337 ARG 0.003 0.000 ARG E 196 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 896) hydrogen bonds : angle 5.20695 ( 2355) covalent geometry : bond 0.00318 (21924) covalent geometry : angle 0.59305 (29739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8386 (m110) REVERT: B 82 MET cc_start: 0.8532 (mmm) cc_final: 0.7073 (tmm) REVERT: B 86 TRP cc_start: 0.8428 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: B 286 ASP cc_start: 0.6984 (t0) cc_final: 0.6492 (t0) REVERT: B 289 ILE cc_start: 0.9026 (mp) cc_final: 0.8749 (tt) REVERT: B 356 TRP cc_start: 0.7948 (m100) cc_final: 0.7562 (m100) REVERT: C 54 VAL cc_start: 0.8481 (t) cc_final: 0.8226 (m) REVERT: C 217 CYS cc_start: 0.8130 (m) cc_final: 0.7398 (m) REVERT: C 313 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7031 (ttm) REVERT: D 192 ILE cc_start: 0.8849 (tp) cc_final: 0.8490 (tp) REVERT: D 234 SER cc_start: 0.8374 (m) cc_final: 0.7654 (p) REVERT: D 313 MET cc_start: 0.8984 (tpp) cc_final: 0.8534 (ttm) REVERT: E 121 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8388 (tm-30) REVERT: E 244 ASP cc_start: 0.7692 (p0) cc_final: 0.7448 (p0) REVERT: F 217 CYS cc_start: 0.7929 (m) cc_final: 0.7684 (m) REVERT: F 289 ILE cc_start: 0.8766 (mm) cc_final: 0.8464 (mt) REVERT: F 349 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6247 (mp) REVERT: F 355 MET cc_start: 0.7114 (mpp) cc_final: 0.6881 (mpp) REVERT: G 65 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8344 (pp) REVERT: G 68 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7755 (tttt) REVERT: G 103 THR cc_start: 0.9130 (t) cc_final: 0.8920 (t) REVERT: G 121 GLN cc_start: 0.8118 (tt0) cc_final: 0.7784 (tm-30) REVERT: G 283 MET cc_start: 0.8272 (tpp) cc_final: 0.8061 (mpp) REVERT: G 305 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7308 (mpp) REVERT: G 362 TYR cc_start: 0.7876 (t80) cc_final: 0.7513 (t80) REVERT: G 372 ARG cc_start: 0.7142 (mtm110) cc_final: 0.6893 (mtm110) outliers start: 61 outliers final: 39 residues processed: 317 average time/residue: 0.3443 time to fit residues: 176.6649 Evaluate side-chains 298 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 216 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 chunk 106 optimal weight: 0.0670 chunk 172 optimal weight: 1.9990 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN B 78 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088294 restraints weight = 51591.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.089947 restraints weight = 32879.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090613 restraints weight = 22907.875| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21924 Z= 0.140 Angle : 0.598 7.916 29739 Z= 0.292 Chirality : 0.045 0.156 3281 Planarity : 0.004 0.044 3827 Dihedral : 7.831 101.795 3048 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.80 % Allowed : 16.30 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.17), residues: 2691 helix: 0.38 (0.17), residues: 960 sheet: 0.39 (0.24), residues: 498 loop : 0.00 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 340 HIS 0.006 0.001 HIS F 101 PHE 0.009 0.001 PHE F 255 TYR 0.011 0.001 TYR G 53 ARG 0.003 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 896) hydrogen bonds : angle 5.16576 ( 2355) covalent geometry : bond 0.00325 (21924) covalent geometry : angle 0.59828 (29739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8538 (mmm) cc_final: 0.7007 (tmm) REVERT: B 86 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: B 286 ASP cc_start: 0.7041 (t0) cc_final: 0.6538 (t0) REVERT: B 289 ILE cc_start: 0.9040 (mp) cc_final: 0.8774 (tt) REVERT: B 356 TRP cc_start: 0.7948 (m100) cc_final: 0.7588 (m100) REVERT: C 54 VAL cc_start: 0.8487 (t) cc_final: 0.8233 (m) REVERT: C 217 CYS cc_start: 0.8155 (m) cc_final: 0.7420 (m) REVERT: C 313 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.7008 (ttm) REVERT: C 360 GLN cc_start: 0.8687 (pm20) cc_final: 0.8412 (pm20) REVERT: D 192 ILE cc_start: 0.8852 (tp) cc_final: 0.8495 (tp) REVERT: D 234 SER cc_start: 0.8388 (m) cc_final: 0.7700 (p) REVERT: D 313 MET cc_start: 0.8991 (tpp) cc_final: 0.8562 (ttm) REVERT: E 121 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8389 (tm-30) REVERT: E 132 MET cc_start: 0.7587 (ppp) cc_final: 0.7255 (ppp) REVERT: E 244 ASP cc_start: 0.7743 (p0) cc_final: 0.7543 (p0) REVERT: E 354 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8211 (mp10) REVERT: F 217 CYS cc_start: 0.7969 (m) cc_final: 0.7706 (m) REVERT: F 289 ILE cc_start: 0.8755 (mm) cc_final: 0.8449 (mt) REVERT: F 349 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6295 (mp) REVERT: G 65 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8332 (pp) REVERT: G 103 THR cc_start: 0.9092 (t) cc_final: 0.8834 (t) REVERT: G 121 GLN cc_start: 0.8112 (tt0) cc_final: 0.7820 (tm-30) REVERT: G 305 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7322 (mpp) REVERT: G 362 TYR cc_start: 0.7821 (t80) cc_final: 0.7437 (t80) REVERT: G 372 ARG cc_start: 0.7338 (mtm110) cc_final: 0.6704 (mtm110) outliers start: 64 outliers final: 44 residues processed: 310 average time/residue: 0.2936 time to fit residues: 147.0301 Evaluate side-chains 296 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 226 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087079 restraints weight = 51999.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.088060 restraints weight = 34673.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.089248 restraints weight = 25120.721| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21924 Z= 0.181 Angle : 0.635 9.371 29739 Z= 0.313 Chirality : 0.047 0.178 3281 Planarity : 0.004 0.046 3827 Dihedral : 7.985 105.450 3048 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.75 % Allowed : 16.78 % Favored : 80.47 % 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: 0.10 (0.17), residues: 2691 helix: 0.29 (0.17), residues: 960 sheet: 0.39 (0.24), residues: 478 loop : -0.09 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP D 340 HIS 0.008 0.001 HIS F 101 PHE 0.048 0.001 PHE G 352 TYR 0.022 0.001 TYR G 279 ARG 0.004 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 896) hydrogen bonds : angle 5.23340 ( 2355) covalent geometry : bond 0.00426 (21924) covalent geometry : angle 0.63490 (29739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 266 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 82 MET cc_start: 0.8510 (mmm) cc_final: 0.6800 (tmm) REVERT: B 86 TRP cc_start: 0.8453 (OUTLIER) cc_final: 0.7147 (m-10) REVERT: B 286 ASP cc_start: 0.6923 (t0) cc_final: 0.6407 (t0) REVERT: B 289 ILE cc_start: 0.9068 (mp) cc_final: 0.8806 (tt) REVERT: B 356 TRP cc_start: 0.7979 (m100) cc_final: 0.7684 (m100) REVERT: C 54 VAL cc_start: 0.8567 (t) cc_final: 0.8315 (m) REVERT: C 313 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7013 (ttm) REVERT: D 123 MET cc_start: 0.8628 (tpp) cc_final: 0.8097 (ttm) REVERT: D 192 ILE cc_start: 0.8894 (tp) cc_final: 0.8535 (tp) REVERT: D 234 SER cc_start: 0.8449 (m) cc_final: 0.7763 (p) REVERT: D 313 MET cc_start: 0.8982 (tpp) cc_final: 0.8537 (ttm) REVERT: D 373 LYS cc_start: 0.8000 (tptm) cc_final: 0.7740 (tptm) REVERT: E 121 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8415 (tm-30) REVERT: E 132 MET cc_start: 0.7593 (ppp) cc_final: 0.7376 (ppp) REVERT: E 186 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8392 (t) REVERT: E 354 GLN cc_start: 0.8450 (tp-100) cc_final: 0.8196 (mp10) REVERT: F 107 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: F 217 CYS cc_start: 0.7975 (m) cc_final: 0.7655 (m) REVERT: F 289 ILE cc_start: 0.8780 (mm) cc_final: 0.8501 (mt) REVERT: F 349 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.5842 (mp) REVERT: F 375 PHE cc_start: 0.4298 (t80) cc_final: 0.3741 (t80) REVERT: G 65 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8360 (pp) REVERT: G 121 GLN cc_start: 0.8126 (tt0) cc_final: 0.7790 (tm-30) REVERT: G 305 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7316 (mpp) REVERT: G 362 TYR cc_start: 0.7774 (t80) cc_final: 0.7317 (t80) REVERT: G 372 ARG cc_start: 0.7267 (mtm110) cc_final: 0.6601 (mtm110) outliers start: 63 outliers final: 49 residues processed: 308 average time/residue: 0.2942 time to fit residues: 145.7998 Evaluate side-chains 299 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 19 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 212 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087469 restraints weight = 52329.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088454 restraints weight = 31937.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089355 restraints weight = 25035.899| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21924 Z= 0.174 Angle : 0.637 11.491 29739 Z= 0.314 Chirality : 0.047 0.181 3281 Planarity : 0.004 0.044 3827 Dihedral : 7.993 104.690 3048 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.75 % Allowed : 17.47 % Favored : 79.77 % 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: 0.07 (0.17), residues: 2691 helix: 0.25 (0.17), residues: 960 sheet: 0.34 (0.24), residues: 478 loop : -0.08 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.002 TRP D 340 HIS 0.008 0.001 HIS F 101 PHE 0.039 0.001 PHE G 352 TYR 0.016 0.001 TYR F 143 ARG 0.004 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 896) hydrogen bonds : angle 5.22810 ( 2355) covalent geometry : bond 0.00408 (21924) covalent geometry : angle 0.63682 (29739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 252 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 41 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 82 MET cc_start: 0.8407 (mmm) cc_final: 0.6109 (tmm) REVERT: B 86 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.6838 (m-10) REVERT: B 286 ASP cc_start: 0.6957 (t0) cc_final: 0.6425 (t0) REVERT: B 289 ILE cc_start: 0.9076 (mp) cc_final: 0.8817 (tt) REVERT: B 356 TRP cc_start: 0.8019 (m100) cc_final: 0.7738 (m100) REVERT: C 54 VAL cc_start: 0.8531 (t) cc_final: 0.8291 (m) REVERT: D 123 MET cc_start: 0.8667 (tpp) cc_final: 0.8069 (ttm) REVERT: D 192 ILE cc_start: 0.8919 (tp) cc_final: 0.8544 (tp) REVERT: D 234 SER cc_start: 0.8390 (m) cc_final: 0.7711 (p) REVERT: D 313 MET cc_start: 0.8969 (tpp) cc_final: 0.8541 (ttm) REVERT: E 121 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8431 (tm-30) REVERT: E 186 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8350 (t) REVERT: F 107 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: F 143 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5765 (t80) REVERT: F 162 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8295 (m-40) REVERT: F 217 CYS cc_start: 0.7988 (m) cc_final: 0.7668 (m) REVERT: F 289 ILE cc_start: 0.8818 (mm) cc_final: 0.8547 (mt) REVERT: F 349 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.5961 (mp) REVERT: F 375 PHE cc_start: 0.4364 (t80) cc_final: 0.3774 (t80) REVERT: G 121 GLN cc_start: 0.8134 (tt0) cc_final: 0.7793 (tm-30) REVERT: G 305 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7354 (mpp) REVERT: G 362 TYR cc_start: 0.7810 (t80) cc_final: 0.7303 (t80) REVERT: G 372 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6624 (mtm110) outliers start: 63 outliers final: 48 residues processed: 294 average time/residue: 0.2909 time to fit residues: 139.0188 Evaluate side-chains 295 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 143 TYR Chi-restraints excluded: chain F residue 162 ASN Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 9 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 262 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 260 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089401 restraints weight = 51522.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.091251 restraints weight = 29914.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091619 restraints weight = 20936.621| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21924 Z= 0.121 Angle : 0.611 11.217 29739 Z= 0.298 Chirality : 0.045 0.191 3281 Planarity : 0.004 0.047 3827 Dihedral : 7.755 99.499 3048 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.10 % Allowed : 18.30 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.17), residues: 2691 helix: 0.37 (0.17), residues: 960 sheet: 0.38 (0.24), residues: 478 loop : -0.00 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP D 340 HIS 0.010 0.001 HIS F 101 PHE 0.037 0.001 PHE G 352 TYR 0.015 0.001 TYR D 362 ARG 0.004 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 896) hydrogen bonds : angle 5.07905 ( 2355) covalent geometry : bond 0.00282 (21924) covalent geometry : angle 0.61129 (29739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 2.478 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: B 82 MET cc_start: 0.8260 (mmm) cc_final: 0.6055 (tmm) REVERT: B 86 TRP cc_start: 0.8381 (OUTLIER) cc_final: 0.6736 (m-10) REVERT: B 286 ASP cc_start: 0.6918 (t0) cc_final: 0.6490 (t0) REVERT: B 289 ILE cc_start: 0.9045 (mp) cc_final: 0.8786 (tt) REVERT: B 356 TRP cc_start: 0.8004 (m100) cc_final: 0.7774 (m100) REVERT: C 54 VAL cc_start: 0.8378 (t) cc_final: 0.8132 (m) REVERT: C 121 GLN cc_start: 0.7266 (tm-30) cc_final: 0.7061 (tm-30) REVERT: C 123 MET cc_start: 0.8007 (ttm) cc_final: 0.7804 (ttm) REVERT: C 217 CYS cc_start: 0.7971 (m) cc_final: 0.7199 (m) REVERT: C 313 MET cc_start: 0.7223 (ttm) cc_final: 0.6938 (ttm) REVERT: D 123 MET cc_start: 0.8501 (tpp) cc_final: 0.7934 (ttm) REVERT: D 192 ILE cc_start: 0.8906 (tp) cc_final: 0.8546 (tp) REVERT: D 234 SER cc_start: 0.8313 (m) cc_final: 0.7650 (p) REVERT: D 313 MET cc_start: 0.8876 (tpp) cc_final: 0.8515 (ttm) REVERT: E 186 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8358 (t) REVERT: E 328 LYS cc_start: 0.7745 (pptt) cc_final: 0.7188 (ptmm) REVERT: F 217 CYS cc_start: 0.7717 (m) cc_final: 0.7510 (m) REVERT: F 289 ILE cc_start: 0.8776 (mm) cc_final: 0.8400 (mt) REVERT: F 349 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6273 (mp) REVERT: F 375 PHE cc_start: 0.4423 (t80) cc_final: 0.3884 (t80) REVERT: G 305 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7197 (mpp) REVERT: G 362 TYR cc_start: 0.7589 (t80) cc_final: 0.7091 (t80) outliers start: 48 outliers final: 35 residues processed: 299 average time/residue: 0.3151 time to fit residues: 153.1847 Evaluate side-chains 283 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 44 MET Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 173 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 264 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 0.6980 chunk 259 optimal weight: 0.0570 chunk 109 optimal weight: 0.0980 chunk 226 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.090617 restraints weight = 51781.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.091760 restraints weight = 32128.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092802 restraints weight = 22857.601| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21924 Z= 0.108 Angle : 0.614 11.074 29739 Z= 0.300 Chirality : 0.045 0.201 3281 Planarity : 0.004 0.051 3827 Dihedral : 7.556 94.213 3048 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.79 % Allowed : 18.79 % Favored : 79.42 % 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: 0.29 (0.17), residues: 2691 helix: 0.41 (0.17), residues: 960 sheet: 0.46 (0.24), residues: 478 loop : 0.07 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP D 340 HIS 0.007 0.001 HIS F 101 PHE 0.036 0.001 PHE G 352 TYR 0.061 0.001 TYR G 279 ARG 0.004 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 896) hydrogen bonds : angle 4.98130 ( 2355) covalent geometry : bond 0.00246 (21924) covalent geometry : angle 0.61373 (29739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5382 Ramachandran restraints generated. 2691 Oldfield, 0 Emsley, 2691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8376 (mmm) cc_final: 0.6048 (tmm) REVERT: B 86 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.6780 (m-10) REVERT: B 286 ASP cc_start: 0.6915 (t0) cc_final: 0.6406 (t0) REVERT: B 356 TRP cc_start: 0.7971 (m100) cc_final: 0.7671 (m100) REVERT: C 54 VAL cc_start: 0.8248 (t) cc_final: 0.8025 (m) REVERT: C 121 GLN cc_start: 0.7168 (tm-30) cc_final: 0.6923 (tm-30) REVERT: C 123 MET cc_start: 0.8169 (ttm) cc_final: 0.7924 (ttm) REVERT: C 217 CYS cc_start: 0.8092 (m) cc_final: 0.7299 (m) REVERT: C 313 MET cc_start: 0.7378 (ttm) cc_final: 0.7098 (ttm) REVERT: D 123 MET cc_start: 0.8580 (tpp) cc_final: 0.7632 (ttm) REVERT: D 192 ILE cc_start: 0.8775 (tp) cc_final: 0.8420 (tp) REVERT: D 234 SER cc_start: 0.8432 (m) cc_final: 0.7810 (p) REVERT: D 313 MET cc_start: 0.8877 (tpp) cc_final: 0.8529 (ttm) REVERT: E 132 MET cc_start: 0.7857 (ppp) cc_final: 0.7085 (ppp) REVERT: E 328 LYS cc_start: 0.7876 (pptt) cc_final: 0.7235 (ptmm) REVERT: F 107 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: F 217 CYS cc_start: 0.7804 (m) cc_final: 0.7586 (m) REVERT: F 289 ILE cc_start: 0.8755 (mm) cc_final: 0.8387 (mt) REVERT: F 349 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6093 (mp) REVERT: F 375 PHE cc_start: 0.4319 (t80) cc_final: 0.3753 (t80) REVERT: G 11 ASP cc_start: 0.8428 (t0) cc_final: 0.8026 (m-30) REVERT: G 279 TYR cc_start: 0.7698 (t80) cc_final: 0.7292 (t80) REVERT: G 305 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7199 (mpp) REVERT: G 362 TYR cc_start: 0.7783 (t80) cc_final: 0.7327 (t80) outliers start: 41 outliers final: 30 residues processed: 298 average time/residue: 0.3169 time to fit residues: 150.9745 Evaluate side-chains 281 residues out of total 2289 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 201 VAL Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 305 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 16 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088353 restraints weight = 51813.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.089901 restraints weight = 34818.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.090587 restraints weight = 23503.103| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21924 Z= 0.158 Angle : 0.642 11.045 29739 Z= 0.316 Chirality : 0.046 0.191 3281 Planarity : 0.004 0.052 3827 Dihedral : 7.712 99.614 3048 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.01 % Allowed : 18.83 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2691 helix: 0.39 (0.17), residues: 960 sheet: 0.45 (0.25), residues: 478 loop : -0.02 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.003 TRP D 340 HIS 0.009 0.001 HIS F 101 PHE 0.034 0.001 PHE G 352 TYR 0.044 0.001 TYR G 279 ARG 0.010 0.000 ARG A 348 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 896) hydrogen bonds : angle 5.02348 ( 2355) covalent geometry : bond 0.00376 (21924) covalent geometry : angle 0.64191 (29739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.25 seconds wall clock time: 119 minutes 6.16 seconds (7146.16 seconds total)