Starting phenix.real_space_refine on Wed Jun 18 07:09:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1n_39731/06_2025/8z1n_39731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1n_39731/06_2025/8z1n_39731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z1n_39731/06_2025/8z1n_39731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1n_39731/06_2025/8z1n_39731.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1n_39731/06_2025/8z1n_39731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1n_39731/06_2025/8z1n_39731.cif" } resolution = 3.18 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= 0.009 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: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 13119 2.51 5 N 3618 2.21 5 O 3974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 20789 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3454 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 443} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "F" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "B" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3467 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 443} Time building chain proxies: 11.97, per 1000 atoms: 0.58 Number of scatterers: 20789 At special positions: 0 Unit cell: (116.63, 120.91, 111.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 3974 8.00 N 3618 7.00 C 13119 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: 4.69 Conformation dependent library (CDL) restraints added in 2.8 seconds 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 14 sheets defined 53.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.588A pdb=" N SER D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 32 through 41 removed outlier: 4.111A pdb=" N ALA D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 removed outlier: 3.822A pdb=" N PHE D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 141 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 158 through 174 Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 199 through 213 Processing helix chain 'D' and resid 231 through 243 removed outlier: 3.969A pdb=" N TYR D 235 " --> pdb=" O ASN D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.774A pdb=" N VAL D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 285 through 291' Processing helix chain 'D' and resid 291 through 296 removed outlier: 4.089A pdb=" N ASP D 296 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 Processing helix chain 'D' and resid 350 through 364 Processing helix chain 'D' and resid 381 through 396 Processing helix chain 'D' and resid 400 through 426 Processing helix chain 'D' and resid 436 through 457 Processing helix chain 'E' and resid 7 through 24 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 32 through 41 removed outlier: 4.195A pdb=" N ALA E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 38 " --> pdb=" O ARG E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.836A pdb=" N PHE E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 141 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 192 through 213 removed outlier: 5.580A pdb=" N VAL E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 243 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 285 through 291 removed outlier: 3.656A pdb=" N VAL E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 296 removed outlier: 4.062A pdb=" N ASP E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 Processing helix chain 'E' and resid 350 through 364 Processing helix chain 'E' and resid 381 through 396 Processing helix chain 'E' and resid 400 through 426 removed outlier: 4.403A pdb=" N ASN E 418 " --> pdb=" O SER E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 457 Processing helix chain 'F' and resid 7 through 24 removed outlier: 3.516A pdb=" N SER F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 32 through 41 removed outlier: 4.259A pdb=" N ALA F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 107 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 158 through 174 Processing helix chain 'F' and resid 192 through 211 Processing helix chain 'F' and resid 231 through 243 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 285 through 291 removed outlier: 3.683A pdb=" N VAL F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 285 through 291' Processing helix chain 'F' and resid 291 through 297 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.813A pdb=" N VAL F 308 " --> pdb=" O ARG F 305 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL F 310 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 381 through 396 Processing helix chain 'F' and resid 400 through 426 Processing helix chain 'F' and resid 436 through 457 Processing helix chain 'B' and resid 7 through 24 removed outlier: 3.605A pdb=" N SER B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 33 through 41 removed outlier: 3.576A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 removed outlier: 3.831A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 192 through 213 removed outlier: 4.932A pdb=" N GLY B 198 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 243 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 285 through 291 removed outlier: 3.552A pdb=" N ASP B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.903A pdb=" N VAL B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL B 310 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 336 Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 381 through 388 removed outlier: 3.657A pdb=" N VAL B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 400 through 426 removed outlier: 4.506A pdb=" N ASN B 418 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.680A pdb=" N SER C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 31 through 34 Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.734A pdb=" N VAL C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 removed outlier: 3.863A pdb=" N PHE C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.973A pdb=" N GLY C 188 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 213 removed outlier: 4.598A pdb=" N VAL C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 243 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 284 through 290 removed outlier: 4.068A pdb=" N VAL C 289 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 Processing helix chain 'C' and resid 305 through 309 removed outlier: 3.986A pdb=" N VAL C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 336 Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 381 through 396 Processing helix chain 'C' and resid 400 through 426 Processing helix chain 'C' and resid 436 through 457 Processing helix chain 'A' and resid 7 through 24 removed outlier: 3.686A pdb=" N SER A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 Processing helix chain 'A' and resid 33 through 41 removed outlier: 3.849A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.830A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 141 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 193 through 213 removed outlier: 4.308A pdb=" N GLY A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.233A pdb=" N TYR A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.506A pdb=" N VAL A 289 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 400 through 427 Processing helix chain 'A' and resid 437 through 457 Processing sheet with id=AA1, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.533A pdb=" N GLY D 112 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 112 " --> pdb=" O PHE B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 246 through 247 removed outlier: 3.506A pdb=" N VAL D 224 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG D 223 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU D 317 " --> pdb=" O ARG D 223 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 225 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 255 through 259 Processing sheet with id=AA4, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.268A pdb=" N ARG E 82 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY E 112 " --> pdb=" O PHE E 70 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY A 112 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 82 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 246 through 250 removed outlier: 6.300A pdb=" N VAL E 224 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 249 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG E 223 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU E 317 " --> pdb=" O ARG E 223 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA E 225 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA E 316 " --> pdb=" O ALA E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 255 through 259 removed outlier: 3.806A pdb=" N LEU E 301 " --> pdb=" O SER E 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.296A pdb=" N ARG F 82 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY F 112 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE F 70 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY C 112 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG C 82 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 246 through 247 removed outlier: 6.134A pdb=" N ARG F 223 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU F 317 " --> pdb=" O ARG F 223 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA F 225 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE F 341 " --> pdb=" O ALA F 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 255 through 259 removed outlier: 3.580A pdb=" N LEU F 301 " --> pdb=" O SER F 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.625A pdb=" N SER B 227 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA B 316 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 255 through 259 Processing sheet with id=AB3, first strand: chain 'C' and resid 246 through 250 removed outlier: 6.337A pdb=" N VAL C 224 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER C 249 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG C 223 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA C 316 " --> pdb=" O ALA C 342 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 341 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 255 through 259 Processing sheet with id=AB5, first strand: chain 'A' and resid 298 through 302 removed outlier: 7.988A pdb=" N VAL A 248 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 224 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 250 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE A 226 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG A 223 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA A 316 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 341 " --> pdb=" O ALA A 373 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3372 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: 7.02 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4482 1.33 - 1.45: 6227 1.45 - 1.58: 10373 1.58 - 1.71: 0 1.71 - 1.83: 126 Bond restraints: 21208 Sorted by residual: bond pdb=" C VAL D 46 " pdb=" O VAL D 46 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.07e-02 8.73e+03 1.01e+01 bond pdb=" C PHE F 97 " pdb=" O PHE F 97 " ideal model delta sigma weight residual 1.236 1.265 -0.028 1.15e-02 7.56e+03 6.11e+00 bond pdb=" CA SER F 90 " pdb=" CB SER F 90 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.55e-02 4.16e+03 5.94e+00 bond pdb=" C ARG F 45 " pdb=" O ARG F 45 " ideal model delta sigma weight residual 1.235 1.205 0.029 1.25e-02 6.40e+03 5.51e+00 bond pdb=" C GLY A 115 " pdb=" O GLY A 115 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.20e-02 6.94e+03 5.17e+00 ... (remaining 21203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 27826 1.90 - 3.80: 807 3.80 - 5.70: 45 5.70 - 7.60: 17 7.60 - 9.50: 2 Bond angle restraints: 28697 Sorted by residual: angle pdb=" N PRO C 269 " pdb=" CD PRO C 269 " pdb=" CG PRO C 269 " ideal model delta sigma weight residual 103.20 93.84 9.36 1.50e+00 4.44e-01 3.89e+01 angle pdb=" N GLU B 389 " pdb=" CA GLU B 389 " pdb=" C GLU B 389 " ideal model delta sigma weight residual 108.96 102.19 6.77 1.49e+00 4.50e-01 2.06e+01 angle pdb=" CB GLU D 98 " pdb=" CG GLU D 98 " pdb=" CD GLU D 98 " ideal model delta sigma weight residual 112.60 119.91 -7.31 1.70e+00 3.46e-01 1.85e+01 angle pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " pdb=" CD GLU A 98 " ideal model delta sigma weight residual 112.60 119.89 -7.29 1.70e+00 3.46e-01 1.84e+01 angle pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " pdb=" CD GLU B 98 " ideal model delta sigma weight residual 112.60 119.64 -7.04 1.70e+00 3.46e-01 1.71e+01 ... (remaining 28692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 10939 17.83 - 35.65: 1205 35.65 - 53.48: 258 53.48 - 71.30: 86 71.30 - 89.13: 33 Dihedral angle restraints: 12521 sinusoidal: 4776 harmonic: 7745 Sorted by residual: dihedral pdb=" CA CYS E 415 " pdb=" C CYS E 415 " pdb=" N PHE E 416 " pdb=" CA PHE E 416 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASN C 109 " pdb=" C ASN C 109 " pdb=" N MET C 110 " pdb=" CA MET C 110 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA CYS F 415 " pdb=" C CYS F 415 " pdb=" N PHE F 416 " pdb=" CA PHE F 416 " ideal model delta harmonic sigma weight residual 180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 12518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1516 0.039 - 0.077: 1031 0.077 - 0.115: 449 0.115 - 0.154: 102 0.154 - 0.192: 21 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CA GLU B 206 " pdb=" N GLU B 206 " pdb=" C GLU B 206 " pdb=" CB GLU B 206 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA THR B 428 " pdb=" N THR B 428 " pdb=" C THR B 428 " pdb=" CB THR B 428 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA TYR B 426 " pdb=" N TYR B 426 " pdb=" C TYR B 426 " pdb=" CB TYR B 426 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 3116 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 67 " 0.247 9.50e-02 1.11e+02 1.13e-01 1.42e+01 pdb=" NE ARG A 67 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 67 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 67 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 67 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 50 " -0.256 9.50e-02 1.11e+02 1.16e-01 1.08e+01 pdb=" NE ARG C 50 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 50 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG C 50 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 50 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 76 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C PRO F 76 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO F 76 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR F 77 " -0.018 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 502 2.68 - 3.24: 21516 3.24 - 3.79: 34695 3.79 - 4.35: 47345 4.35 - 4.90: 76251 Nonbonded interactions: 180309 Sorted by model distance: nonbonded pdb=" OD2 ASP C 147 " pdb=" OG SER A 175 " model vdw 2.130 3.040 nonbonded pdb=" OE1 GLU D 44 " pdb=" OH TYR D 77 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLU C 44 " pdb=" OH TYR C 77 " model vdw 2.196 3.040 nonbonded pdb=" NH2 ARG D 170 " pdb=" OE1 GLN F 456 " model vdw 2.216 3.120 nonbonded pdb=" OG SER F 229 " pdb=" OD2 ASP F 252 " model vdw 2.217 3.040 ... (remaining 180304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = (chain 'B' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = (chain 'C' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) selection = (chain 'F' and (resid 1 through 194 or (resid 195 through 197 and (name N or nam \ e CA or name C or name O or name CB )) or resid 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 460)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 46.390 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 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 : 0.008 0.056 21208 Z= 0.480 Angle : 0.821 9.498 28697 Z= 0.512 Chirality : 0.057 0.192 3119 Planarity : 0.009 0.116 3784 Dihedral : 16.730 89.126 7601 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.39 % Favored : 94.25 % Rotamer: Outliers : 0.95 % Allowed : 21.87 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2748 helix: 0.93 (0.14), residues: 1368 sheet: -2.07 (0.26), residues: 396 loop : -1.09 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP C 460 HIS 0.010 0.003 HIS A 360 PHE 0.027 0.006 PHE F 416 TYR 0.023 0.005 TYR B 199 ARG 0.045 0.004 ARG A 67 Details of bonding type rmsd hydrogen bonds : bond 0.14089 ( 1140) hydrogen bonds : angle 6.36982 ( 3372) covalent geometry : bond 0.00779 (21208) covalent geometry : angle 0.82055 (28697) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 455 ASP cc_start: 0.7247 (t70) cc_final: 0.6917 (t0) REVERT: F 78 LYS cc_start: 0.7307 (tmtt) cc_final: 0.7098 (tptp) REVERT: F 426 TYR cc_start: 0.5172 (t80) cc_final: 0.4936 (t80) REVERT: C 32 GLU cc_start: 0.6717 (tt0) cc_final: 0.6508 (mp0) outliers start: 20 outliers final: 10 residues processed: 183 average time/residue: 0.3147 time to fit residues: 94.6844 Evaluate side-chains 170 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain E residue 309 HIS Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 412 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain A residue 70 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS E 331 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS C 143 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.203188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155512 restraints weight = 27184.171| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.05 r_work: 0.3641 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21208 Z= 0.131 Angle : 0.530 7.480 28697 Z= 0.286 Chirality : 0.041 0.140 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.894 56.984 2973 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.08 % Favored : 95.67 % Rotamer: Outliers : 3.52 % Allowed : 19.16 % Favored : 77.32 % 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: 0.14 (0.16), residues: 2748 helix: 1.34 (0.14), residues: 1386 sheet: -1.58 (0.29), residues: 354 loop : -0.97 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.004 0.001 HIS C 360 PHE 0.016 0.002 PHE F 416 TYR 0.021 0.002 TYR E 426 ARG 0.004 0.001 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.04433 ( 1140) hydrogen bonds : angle 5.01065 ( 3372) covalent geometry : bond 0.00278 (21208) covalent geometry : angle 0.53021 (28697) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 205 time to evaluate : 2.089 Fit side-chains revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: D 226 ILE cc_start: 0.6029 (OUTLIER) cc_final: 0.5751 (mt) REVERT: D 329 GLU cc_start: 0.8099 (mp0) cc_final: 0.7532 (mp0) REVERT: E 307 TRP cc_start: 0.6869 (m100) cc_final: 0.6606 (m100) REVERT: E 403 GLU cc_start: 0.6432 (mm-30) cc_final: 0.6032 (tp30) REVERT: E 417 GLN cc_start: 0.6043 (mt0) cc_final: 0.5732 (mm-40) REVERT: F 78 LYS cc_start: 0.7853 (tmtt) cc_final: 0.7511 (tptp) REVERT: B 301 LEU cc_start: 0.5419 (mm) cc_final: 0.5116 (mt) REVERT: B 309 HIS cc_start: 0.3815 (p90) cc_final: 0.3537 (p-80) REVERT: B 390 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.4533 (pmm) REVERT: B 403 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5883 (tp30) REVERT: B 412 MET cc_start: 0.3180 (ppp) cc_final: 0.2831 (ppp) REVERT: C 149 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6972 (m-30) REVERT: C 206 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7072 (mt-10) REVERT: C 208 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6273 (mmm) REVERT: C 219 PHE cc_start: 0.6254 (OUTLIER) cc_final: 0.5764 (m-80) REVERT: A 219 PHE cc_start: 0.6256 (OUTLIER) cc_final: 0.5481 (m-80) outliers start: 74 outliers final: 31 residues processed: 259 average time/residue: 0.2767 time to fit residues: 117.9506 Evaluate side-chains 212 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 127 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS D 379 ASN ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 71 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.199336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.149116 restraints weight = 27145.180| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.93 r_work: 0.3603 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 21208 Z= 0.222 Angle : 0.593 7.308 28697 Z= 0.320 Chirality : 0.043 0.248 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.578 47.118 2959 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.60 % Favored : 94.14 % Rotamer: Outliers : 4.71 % Allowed : 18.93 % Favored : 76.37 % 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: -0.02 (0.16), residues: 2748 helix: 1.19 (0.14), residues: 1374 sheet: -1.62 (0.28), residues: 354 loop : -0.98 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 176 HIS 0.016 0.001 HIS F 207 PHE 0.018 0.003 PHE F 66 TYR 0.021 0.002 TYR F 77 ARG 0.003 0.000 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 1140) hydrogen bonds : angle 5.02436 ( 3372) covalent geometry : bond 0.00516 (21208) covalent geometry : angle 0.59272 (28697) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 187 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: D 1 MET cc_start: 0.5086 (mtp) cc_final: 0.4854 (mmp) REVERT: D 226 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5839 (mt) REVERT: D 329 GLU cc_start: 0.8109 (mp0) cc_final: 0.7592 (mp0) REVERT: E 238 LEU cc_start: 0.5432 (tt) cc_final: 0.4728 (mp) REVERT: E 307 TRP cc_start: 0.6971 (m100) cc_final: 0.6575 (m100) REVERT: E 403 GLU cc_start: 0.6399 (mm-30) cc_final: 0.6050 (tp30) REVERT: B 301 LEU cc_start: 0.5416 (mm) cc_final: 0.5076 (mt) REVERT: B 309 HIS cc_start: 0.3854 (p90) cc_final: 0.3608 (p-80) REVERT: B 389 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5853 (tp30) REVERT: B 390 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.5308 (pmm) REVERT: B 403 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5850 (tp30) REVERT: B 412 MET cc_start: 0.3069 (ppp) cc_final: 0.2640 (ppp) REVERT: C 56 ASP cc_start: 0.8321 (m-30) cc_final: 0.7981 (m-30) REVERT: C 206 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: C 219 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5767 (m-80) REVERT: A 206 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: A 219 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.5428 (m-80) REVERT: A 258 ILE cc_start: 0.7160 (OUTLIER) cc_final: 0.6721 (mp) outliers start: 99 outliers final: 51 residues processed: 264 average time/residue: 0.2921 time to fit residues: 127.4967 Evaluate side-chains 227 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 198 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 110 optimal weight: 0.0270 chunk 121 optimal weight: 5.9990 overall best weight: 0.7450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.203095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155728 restraints weight = 27360.152| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.97 r_work: 0.3654 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21208 Z= 0.123 Angle : 0.511 7.755 28697 Z= 0.274 Chirality : 0.040 0.147 3119 Planarity : 0.003 0.042 3784 Dihedral : 4.330 47.308 2959 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 3.76 % Allowed : 19.83 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.16), residues: 2748 helix: 1.37 (0.14), residues: 1386 sheet: -1.50 (0.29), residues: 354 loop : -0.92 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 176 HIS 0.011 0.001 HIS F 207 PHE 0.017 0.002 PHE A 294 TYR 0.020 0.002 TYR F 235 ARG 0.003 0.000 ARG B 361 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 1140) hydrogen bonds : angle 4.79842 ( 3372) covalent geometry : bond 0.00267 (21208) covalent geometry : angle 0.51069 (28697) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 2.210 Fit side-chains revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: D 56 ASP cc_start: 0.7995 (m-30) cc_final: 0.7740 (m-30) REVERT: D 329 GLU cc_start: 0.8035 (mp0) cc_final: 0.7524 (mp0) REVERT: E 268 THR cc_start: 0.6325 (OUTLIER) cc_final: 0.6094 (t) REVERT: E 307 TRP cc_start: 0.6928 (m100) cc_final: 0.6622 (m100) REVERT: E 403 GLU cc_start: 0.6451 (mm-30) cc_final: 0.6107 (tp30) REVERT: E 426 TYR cc_start: 0.5233 (t80) cc_final: 0.4468 (t80) REVERT: F 206 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6364 (mt-10) REVERT: F 301 LEU cc_start: 0.5740 (mm) cc_final: 0.5453 (mt) REVERT: F 426 TYR cc_start: 0.4704 (t80) cc_final: 0.4468 (m-10) REVERT: B 155 ILE cc_start: 0.8254 (mt) cc_final: 0.7959 (tp) REVERT: B 187 TRP cc_start: 0.7465 (p90) cc_final: 0.6979 (p90) REVERT: B 301 LEU cc_start: 0.5513 (mm) cc_final: 0.5157 (mt) REVERT: B 389 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5744 (tp30) REVERT: B 403 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5884 (tp30) REVERT: B 412 MET cc_start: 0.2567 (ppp) cc_final: 0.2335 (ppp) REVERT: C 56 ASP cc_start: 0.8208 (m-30) cc_final: 0.7884 (m-30) REVERT: C 149 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: C 187 TRP cc_start: 0.6231 (p90) cc_final: 0.5849 (p90) REVERT: C 206 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: C 208 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6295 (mmm) REVERT: C 219 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5558 (m-80) REVERT: A 206 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: A 219 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: A 258 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6792 (mp) outliers start: 79 outliers final: 43 residues processed: 252 average time/residue: 0.2774 time to fit residues: 115.0811 Evaluate side-chains 226 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 234 GLN Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 309 HIS Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 187 optimal weight: 4.9990 chunk 192 optimal weight: 0.4980 chunk 76 optimal weight: 0.2980 chunk 275 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 217 optimal weight: 20.0000 chunk 255 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS E 69 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN F 309 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.204112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.154944 restraints weight = 27220.329| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.00 r_work: 0.3667 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21208 Z= 0.117 Angle : 0.505 7.588 28697 Z= 0.271 Chirality : 0.040 0.133 3119 Planarity : 0.003 0.042 3784 Dihedral : 4.180 46.908 2959 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.66 % Favored : 95.12 % Rotamer: Outliers : 3.90 % Allowed : 20.26 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2748 helix: 1.47 (0.14), residues: 1386 sheet: -1.36 (0.29), residues: 342 loop : -0.85 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.009 0.001 HIS F 207 PHE 0.036 0.002 PHE F 340 TYR 0.013 0.001 TYR B 235 ARG 0.002 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1140) hydrogen bonds : angle 4.68913 ( 3372) covalent geometry : bond 0.00253 (21208) covalent geometry : angle 0.50501 (28697) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 195 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: D 219 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5643 (m-80) REVERT: D 226 ILE cc_start: 0.5901 (OUTLIER) cc_final: 0.5654 (mt) REVERT: D 329 GLU cc_start: 0.8052 (mp0) cc_final: 0.7511 (mp0) REVERT: E 4 LEU cc_start: 0.8394 (tt) cc_final: 0.7991 (mp) REVERT: E 187 TRP cc_start: 0.6987 (p90) cc_final: 0.6556 (p90) REVERT: E 268 THR cc_start: 0.6287 (OUTLIER) cc_final: 0.6053 (t) REVERT: E 301 LEU cc_start: 0.5861 (mm) cc_final: 0.5437 (mt) REVERT: E 307 TRP cc_start: 0.6886 (m100) cc_final: 0.6602 (m100) REVERT: E 403 GLU cc_start: 0.6425 (mm-30) cc_final: 0.6096 (tp30) REVERT: E 426 TYR cc_start: 0.5292 (t80) cc_final: 0.5067 (t80) REVERT: F 98 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7248 (mm-30) REVERT: F 206 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6342 (mt-10) REVERT: F 301 LEU cc_start: 0.5670 (mm) cc_final: 0.5383 (mt) REVERT: B 155 ILE cc_start: 0.8235 (mt) cc_final: 0.7948 (tp) REVERT: B 187 TRP cc_start: 0.7363 (p90) cc_final: 0.6679 (p90) REVERT: B 211 HIS cc_start: 0.4882 (m-70) cc_final: 0.4670 (m170) REVERT: B 301 LEU cc_start: 0.5599 (mm) cc_final: 0.5198 (mt) REVERT: B 403 GLU cc_start: 0.6247 (mm-30) cc_final: 0.5889 (tp30) REVERT: C 56 ASP cc_start: 0.8150 (m-30) cc_final: 0.7791 (m-30) REVERT: C 149 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6917 (m-30) REVERT: C 206 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: C 208 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6241 (mmm) REVERT: C 219 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5415 (m-80) REVERT: A 206 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: A 219 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5314 (m-80) REVERT: A 258 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6778 (mp) outliers start: 82 outliers final: 48 residues processed: 257 average time/residue: 0.2854 time to fit residues: 120.5152 Evaluate side-chains 240 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 180 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 371 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 252 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 242 optimal weight: 0.0170 chunk 111 optimal weight: 0.3980 chunk 175 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS B 309 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.204715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156158 restraints weight = 27070.954| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.97 r_work: 0.3670 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21208 Z= 0.116 Angle : 0.507 9.485 28697 Z= 0.270 Chirality : 0.040 0.312 3119 Planarity : 0.003 0.042 3784 Dihedral : 4.127 46.546 2959 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.41 % Rotamer: Outliers : 4.18 % Allowed : 20.16 % Favored : 75.65 % 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: 0.44 (0.17), residues: 2748 helix: 1.52 (0.14), residues: 1392 sheet: -1.31 (0.29), residues: 342 loop : -0.79 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 187 HIS 0.008 0.001 HIS F 207 PHE 0.024 0.002 PHE F 340 TYR 0.029 0.002 TYR F 235 ARG 0.006 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 1140) hydrogen bonds : angle 4.62169 ( 3372) covalent geometry : bond 0.00249 (21208) covalent geometry : angle 0.50726 (28697) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 191 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: D 219 PHE cc_start: 0.6204 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: D 226 ILE cc_start: 0.5919 (OUTLIER) cc_final: 0.5678 (mt) REVERT: D 455 ASP cc_start: 0.8118 (t0) cc_final: 0.7903 (t0) REVERT: E 4 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7989 (mp) REVERT: E 187 TRP cc_start: 0.7018 (p90) cc_final: 0.6565 (p90) REVERT: E 268 THR cc_start: 0.6266 (OUTLIER) cc_final: 0.6051 (t) REVERT: E 301 LEU cc_start: 0.5869 (mm) cc_final: 0.5469 (mt) REVERT: E 307 TRP cc_start: 0.6887 (m100) cc_final: 0.6661 (m100) REVERT: E 334 ILE cc_start: 0.7890 (mt) cc_final: 0.7631 (tt) REVERT: E 403 GLU cc_start: 0.6452 (mm-30) cc_final: 0.6118 (tp30) REVERT: F 199 TYR cc_start: 0.4189 (m-10) cc_final: 0.3970 (m-10) REVERT: F 206 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6404 (mt-10) REVERT: F 298 PHE cc_start: 0.4732 (OUTLIER) cc_final: 0.2898 (m-80) REVERT: F 301 LEU cc_start: 0.5645 (mm) cc_final: 0.5355 (mt) REVERT: B 155 ILE cc_start: 0.8224 (mt) cc_final: 0.7920 (tp) REVERT: B 187 TRP cc_start: 0.7369 (p90) cc_final: 0.6800 (p90) REVERT: B 301 LEU cc_start: 0.5829 (mm) cc_final: 0.5413 (mt) REVERT: B 309 HIS cc_start: 0.4481 (p90) cc_final: 0.4279 (p-80) REVERT: B 403 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5923 (tp30) REVERT: B 412 MET cc_start: 0.2300 (ppp) cc_final: 0.2072 (ppp) REVERT: C 56 ASP cc_start: 0.8116 (m-30) cc_final: 0.7749 (m-30) REVERT: C 149 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: C 208 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6541 (mmm) REVERT: C 219 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.5361 (m-10) REVERT: C 329 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7354 (pt0) REVERT: A 206 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: A 219 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5342 (m-80) REVERT: A 258 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6791 (mp) outliers start: 88 outliers final: 50 residues processed: 258 average time/residue: 0.2760 time to fit residues: 117.2097 Evaluate side-chains 242 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 179 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 371 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 150 optimal weight: 0.7980 chunk 263 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 205 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 overall best weight: 1.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS E 69 GLN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.203151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156350 restraints weight = 27061.929| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.93 r_work: 0.3639 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21208 Z= 0.152 Angle : 0.539 7.855 28697 Z= 0.287 Chirality : 0.041 0.203 3119 Planarity : 0.004 0.041 3784 Dihedral : 4.218 43.733 2959 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.91 % Favored : 94.91 % Rotamer: Outliers : 3.99 % Allowed : 20.45 % Favored : 75.56 % 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: 0.40 (0.17), residues: 2748 helix: 1.47 (0.14), residues: 1386 sheet: -1.25 (0.29), residues: 348 loop : -0.81 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 187 HIS 0.008 0.001 HIS F 207 PHE 0.019 0.002 PHE F 340 TYR 0.050 0.002 TYR B 235 ARG 0.006 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1140) hydrogen bonds : angle 4.67025 ( 3372) covalent geometry : bond 0.00348 (21208) covalent geometry : angle 0.53864 (28697) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 193 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: D 219 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5460 (m-80) REVERT: D 226 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5860 (mt) REVERT: D 329 GLU cc_start: 0.8093 (mp0) cc_final: 0.7521 (mp0) REVERT: E 4 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8011 (mp) REVERT: E 187 TRP cc_start: 0.7257 (p90) cc_final: 0.6818 (p90) REVERT: E 268 THR cc_start: 0.6282 (OUTLIER) cc_final: 0.6065 (t) REVERT: E 301 LEU cc_start: 0.5827 (mm) cc_final: 0.5415 (mt) REVERT: E 307 TRP cc_start: 0.6972 (m100) cc_final: 0.6634 (m100) REVERT: E 403 GLU cc_start: 0.6408 (mm-30) cc_final: 0.6090 (tp30) REVERT: F 34 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7848 (mtp180) REVERT: F 206 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6453 (mt-10) REVERT: F 298 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.2916 (m-80) REVERT: F 301 LEU cc_start: 0.5754 (mm) cc_final: 0.5393 (mt) REVERT: B 4 LEU cc_start: 0.8448 (tt) cc_final: 0.8174 (mp) REVERT: B 155 ILE cc_start: 0.8206 (mt) cc_final: 0.7935 (tp) REVERT: B 187 TRP cc_start: 0.7392 (p90) cc_final: 0.6885 (p90) REVERT: B 301 LEU cc_start: 0.6046 (mm) cc_final: 0.5619 (mt) REVERT: B 307 TRP cc_start: 0.6618 (m100) cc_final: 0.6363 (m100) REVERT: B 403 GLU cc_start: 0.6155 (mm-30) cc_final: 0.5824 (tp30) REVERT: B 412 MET cc_start: 0.2274 (ppp) cc_final: 0.2046 (ppp) REVERT: C 56 ASP cc_start: 0.8193 (m-30) cc_final: 0.7801 (m-30) REVERT: C 149 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6965 (m-30) REVERT: C 219 PHE cc_start: 0.6284 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: A 206 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: A 219 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5251 (m-80) REVERT: A 258 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6812 (mp) outliers start: 84 outliers final: 53 residues processed: 261 average time/residue: 0.2992 time to fit residues: 128.7236 Evaluate side-chains 243 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 55 optimal weight: 0.4980 chunk 247 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 155 optimal weight: 0.0870 chunk 232 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 261 optimal weight: 0.6980 chunk 125 optimal weight: 9.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN D 360 HIS E 109 ASN E 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.204126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156018 restraints weight = 27177.595| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.95 r_work: 0.3654 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21208 Z= 0.130 Angle : 0.526 8.320 28697 Z= 0.279 Chirality : 0.040 0.169 3119 Planarity : 0.003 0.041 3784 Dihedral : 3.992 34.736 2955 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.69 % Favored : 95.12 % Rotamer: Outliers : 3.90 % Allowed : 20.78 % Favored : 75.32 % 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: 0.44 (0.16), residues: 2748 helix: 1.50 (0.14), residues: 1386 sheet: -1.22 (0.29), residues: 348 loop : -0.79 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 187 HIS 0.011 0.001 HIS F 309 PHE 0.017 0.002 PHE F 340 TYR 0.039 0.002 TYR B 235 ARG 0.006 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1140) hydrogen bonds : angle 4.62389 ( 3372) covalent geometry : bond 0.00294 (21208) covalent geometry : angle 0.52601 (28697) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 185 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: D 219 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: D 226 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5849 (mt) REVERT: D 329 GLU cc_start: 0.8080 (mp0) cc_final: 0.7500 (mp0) REVERT: E 4 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8009 (mp) REVERT: E 187 TRP cc_start: 0.7281 (p90) cc_final: 0.6737 (p90) REVERT: E 268 THR cc_start: 0.6270 (OUTLIER) cc_final: 0.6052 (t) REVERT: E 301 LEU cc_start: 0.5828 (mm) cc_final: 0.5420 (mt) REVERT: E 307 TRP cc_start: 0.6939 (m100) cc_final: 0.6614 (m100) REVERT: E 412 MET cc_start: 0.2801 (ppp) cc_final: 0.2482 (ppp) REVERT: E 426 TYR cc_start: 0.5666 (t80) cc_final: 0.5364 (t80) REVERT: F 206 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: F 298 PHE cc_start: 0.4757 (OUTLIER) cc_final: 0.2905 (m-80) REVERT: F 301 LEU cc_start: 0.5757 (mm) cc_final: 0.5400 (mt) REVERT: B 4 LEU cc_start: 0.8449 (tt) cc_final: 0.8196 (mp) REVERT: B 155 ILE cc_start: 0.8242 (mt) cc_final: 0.7958 (tp) REVERT: B 187 TRP cc_start: 0.7402 (p90) cc_final: 0.6849 (p90) REVERT: B 301 LEU cc_start: 0.6109 (mm) cc_final: 0.5781 (mt) REVERT: B 307 TRP cc_start: 0.6605 (m100) cc_final: 0.6347 (m100) REVERT: C 56 ASP cc_start: 0.8200 (m-30) cc_final: 0.7818 (m-30) REVERT: C 149 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: C 208 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6282 (mmm) REVERT: C 219 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5360 (m-10) REVERT: A 187 TRP cc_start: 0.6968 (p90) cc_final: 0.6759 (p90) REVERT: A 206 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6776 (mt-10) REVERT: A 219 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5172 (m-80) REVERT: A 258 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6825 (mp) outliers start: 82 outliers final: 58 residues processed: 248 average time/residue: 0.2876 time to fit residues: 116.4598 Evaluate side-chains 246 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 175 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 371 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 118 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 186 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS F 109 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.202371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157088 restraints weight = 27129.508| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.82 r_work: 0.3646 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21208 Z= 0.172 Angle : 0.564 7.954 28697 Z= 0.302 Chirality : 0.042 0.182 3119 Planarity : 0.004 0.041 3784 Dihedral : 4.097 35.692 2955 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 3.71 % Allowed : 21.73 % Favored : 74.56 % 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: 0.33 (0.17), residues: 2748 helix: 1.45 (0.14), residues: 1386 sheet: -1.32 (0.27), residues: 420 loop : -0.81 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 187 HIS 0.021 0.002 HIS E 211 PHE 0.016 0.002 PHE C 166 TYR 0.035 0.002 TYR B 199 ARG 0.005 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1140) hydrogen bonds : angle 4.70954 ( 3372) covalent geometry : bond 0.00396 (21208) covalent geometry : angle 0.56424 (28697) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 178 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: D 219 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5483 (m-80) REVERT: D 226 ILE cc_start: 0.6143 (OUTLIER) cc_final: 0.5888 (mt) REVERT: D 329 GLU cc_start: 0.8134 (mp0) cc_final: 0.7540 (mp0) REVERT: E 4 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 268 THR cc_start: 0.6294 (OUTLIER) cc_final: 0.6079 (t) REVERT: E 301 LEU cc_start: 0.5961 (mm) cc_final: 0.5518 (mt) REVERT: E 307 TRP cc_start: 0.7005 (m100) cc_final: 0.6658 (m100) REVERT: E 426 TYR cc_start: 0.5635 (t80) cc_final: 0.5333 (t80) REVERT: F 206 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: F 298 PHE cc_start: 0.4741 (OUTLIER) cc_final: 0.2933 (m-80) REVERT: F 301 LEU cc_start: 0.5947 (mm) cc_final: 0.5595 (mt) REVERT: B 4 LEU cc_start: 0.8457 (tt) cc_final: 0.8217 (mp) REVERT: B 155 ILE cc_start: 0.8208 (mt) cc_final: 0.7962 (tp) REVERT: B 187 TRP cc_start: 0.7462 (p90) cc_final: 0.6930 (p90) REVERT: B 301 LEU cc_start: 0.5947 (mm) cc_final: 0.5567 (mt) REVERT: B 307 TRP cc_start: 0.6665 (m100) cc_final: 0.6386 (m100) REVERT: B 412 MET cc_start: 0.2346 (ppp) cc_final: 0.2070 (ppp) REVERT: C 56 ASP cc_start: 0.8191 (m-30) cc_final: 0.7798 (m-30) REVERT: C 149 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6961 (m-30) REVERT: C 219 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5405 (m-80) REVERT: A 206 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6833 (mt-10) REVERT: A 219 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5213 (m-80) REVERT: A 258 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6913 (mp) outliers start: 78 outliers final: 57 residues processed: 239 average time/residue: 0.2724 time to fit residues: 107.8870 Evaluate side-chains 237 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 168 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 296 ASP Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 371 TRP Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 216 optimal weight: 5.9990 chunk 196 optimal weight: 0.0670 chunk 259 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 151 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS F 109 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 GLN F 309 HIS ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.205377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157536 restraints weight = 26939.190| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.08 r_work: 0.3679 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21208 Z= 0.114 Angle : 0.521 8.256 28697 Z= 0.277 Chirality : 0.040 0.165 3119 Planarity : 0.003 0.042 3784 Dihedral : 3.926 35.664 2955 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 3.23 % Allowed : 22.49 % Favored : 74.27 % 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: 0.32 (0.17), residues: 2748 helix: 1.33 (0.14), residues: 1434 sheet: -1.15 (0.29), residues: 348 loop : -0.87 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 187 HIS 0.015 0.001 HIS E 211 PHE 0.015 0.001 PHE F 340 TYR 0.041 0.002 TYR B 199 ARG 0.005 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1140) hydrogen bonds : angle 4.59526 ( 3372) covalent geometry : bond 0.00250 (21208) covalent geometry : angle 0.52147 (28697) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5496 Ramachandran restraints generated. 2748 Oldfield, 0 Emsley, 2748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 182 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: D 219 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: D 226 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5739 (mt) REVERT: E 4 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7983 (mp) REVERT: E 268 THR cc_start: 0.6296 (OUTLIER) cc_final: 0.6074 (t) REVERT: E 301 LEU cc_start: 0.5810 (mm) cc_final: 0.5415 (mt) REVERT: E 307 TRP cc_start: 0.6889 (m100) cc_final: 0.6575 (m100) REVERT: E 309 HIS cc_start: 0.4197 (m90) cc_final: 0.3834 (m90) REVERT: F 4 LEU cc_start: 0.8564 (tp) cc_final: 0.8314 (mp) REVERT: F 98 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7244 (mm-30) REVERT: F 206 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6527 (mt-10) REVERT: F 298 PHE cc_start: 0.4769 (OUTLIER) cc_final: 0.2893 (m-80) REVERT: F 301 LEU cc_start: 0.5858 (mm) cc_final: 0.5527 (mt) REVERT: F 331 GLN cc_start: 0.6816 (mm-40) cc_final: 0.6478 (mp10) REVERT: B 4 LEU cc_start: 0.8464 (tt) cc_final: 0.8220 (mp) REVERT: B 78 LYS cc_start: 0.7778 (tmtt) cc_final: 0.7573 (tttp) REVERT: B 155 ILE cc_start: 0.8206 (mt) cc_final: 0.7880 (tp) REVERT: B 187 TRP cc_start: 0.7356 (p90) cc_final: 0.6771 (p90) REVERT: B 301 LEU cc_start: 0.6042 (mm) cc_final: 0.5736 (mt) REVERT: B 307 TRP cc_start: 0.6522 (m100) cc_final: 0.6294 (m100) REVERT: B 412 MET cc_start: 0.2304 (ppp) cc_final: 0.2060 (ppp) REVERT: C 56 ASP cc_start: 0.8175 (m-30) cc_final: 0.7788 (m-30) REVERT: C 109 ASN cc_start: 0.6200 (OUTLIER) cc_final: 0.5343 (p0) REVERT: C 149 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6868 (m-30) REVERT: C 208 MET cc_start: 0.6426 (OUTLIER) cc_final: 0.5947 (mmm) REVERT: C 219 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.5328 (m-10) REVERT: A 206 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6919 (mt-10) REVERT: A 219 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5223 (m-80) REVERT: A 258 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6855 (mp) outliers start: 68 outliers final: 44 residues processed: 234 average time/residue: 0.2980 time to fit residues: 114.4025 Evaluate side-chains 227 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 169 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 309 HIS Chi-restraints excluded: chain D residue 371 TRP Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 208 MET Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 416 PHE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 109 ASN Chi-restraints excluded: chain F residue 206 GLU Chi-restraints excluded: chain F residue 298 PHE Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 410 ASP Chi-restraints excluded: chain B residue 16 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 371 TRP Chi-restraints excluded: chain B residue 390 MET Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 460 TRP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 347 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 100 optimal weight: 0.0060 chunk 253 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 230 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.202943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152073 restraints weight = 27071.705| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.95 r_work: 0.3644 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21208 Z= 0.175 Angle : 0.563 7.452 28697 Z= 0.300 Chirality : 0.042 0.173 3119 Planarity : 0.004 0.041 3784 Dihedral : 4.009 36.034 2955 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.06 % Favored : 94.76 % Rotamer: Outliers : 3.00 % Allowed : 22.63 % Favored : 74.37 % 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: 0.24 (0.17), residues: 2748 helix: 1.27 (0.14), residues: 1428 sheet: -1.27 (0.29), residues: 360 loop : -0.88 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 187 HIS 0.017 0.002 HIS A 207 PHE 0.014 0.002 PHE C 132 TYR 0.038 0.002 TYR A 235 ARG 0.005 0.000 ARG F 142 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 1140) hydrogen bonds : angle 4.63633 ( 3372) covalent geometry : bond 0.00408 (21208) covalent geometry : angle 0.56316 (28697) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12927.20 seconds wall clock time: 221 minutes 29.79 seconds (13289.79 seconds total)