Starting phenix.real_space_refine on Thu Sep 18 22:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z1n_39731/09_2025/8z1n_39731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z1n_39731/09_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_39731/09_2025/8z1n_39731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z1n_39731/09_2025/8z1n_39731.map" model { file = "/net/cci-nas-00/data/ceres_data/8z1n_39731/09_2025/8z1n_39731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z1n_39731/09_2025/8z1n_39731.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'TYR: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: 4.75, per 1000 atoms: 0.23 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: 1.89 Conformation dependent library (CDL) restraints added in 887.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.75 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: 3.65 Time building geometry restraints manager: 2.49 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: 1.310 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.730 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- 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 : 15.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (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 ARG 0.045 0.004 ARG A 67 TYR 0.023 0.005 TYR B 199 PHE 0.027 0.006 PHE F 416 TRP 0.040 0.006 TRP C 460 HIS 0.010 0.003 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00779 (21208) covalent geometry : angle 0.82055 (28697) hydrogen bonds : bond 0.14089 ( 1140) hydrogen bonds : angle 6.36982 ( 3372) *********************** 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 : 0.774 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: 0.1356 time to fit residues: 41.0733 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 : 0.817 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.202618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.151548 restraints weight = 27212.910| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.22 r_work: 0.3647 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0907 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= 0.133 Angle : 0.536 7.449 28697 Z= 0.290 Chirality : 0.041 0.140 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.930 56.925 2973 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 3.42 % Allowed : 19.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.16), residues: 2748 helix: 1.30 (0.14), residues: 1386 sheet: -1.58 (0.29), residues: 354 loop : -1.00 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 361 TYR 0.020 0.002 TYR E 426 PHE 0.017 0.002 PHE F 416 TRP 0.009 0.001 TRP C 176 HIS 0.005 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00290 (21208) covalent geometry : angle 0.53637 (28697) hydrogen bonds : bond 0.04584 ( 1140) hydrogen bonds : angle 5.06659 ( 3372) *********************** 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 273 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 201 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: D 226 ILE cc_start: 0.5871 (OUTLIER) cc_final: 0.5595 (mt) REVERT: D 329 GLU cc_start: 0.8079 (mp0) cc_final: 0.7479 (mp0) REVERT: E 307 TRP cc_start: 0.6820 (m100) cc_final: 0.6550 (m100) REVERT: E 403 GLU cc_start: 0.6427 (mm-30) cc_final: 0.6024 (tp30) REVERT: E 417 GLN cc_start: 0.6101 (mt0) cc_final: 0.5721 (mm-40) REVERT: F 78 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7535 (tptp) REVERT: B 301 LEU cc_start: 0.5311 (mm) cc_final: 0.5004 (mt) REVERT: B 309 HIS cc_start: 0.4028 (p90) cc_final: 0.3755 (p-80) REVERT: B 390 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.4498 (pmm) REVERT: B 403 GLU cc_start: 0.6233 (mm-30) cc_final: 0.5855 (tp30) REVERT: B 412 MET cc_start: 0.3031 (ppp) cc_final: 0.2673 (ppp) REVERT: C 149 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: C 206 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7007 (mt-10) REVERT: C 208 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6225 (mmm) REVERT: C 219 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5791 (m-80) REVERT: A 219 PHE cc_start: 0.6284 (OUTLIER) cc_final: 0.5495 (m-80) outliers start: 72 outliers final: 31 residues processed: 255 average time/residue: 0.1319 time to fit residues: 55.6883 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 : 0.529 ------------------------------------------------------------------------------- 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 310 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 219 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 81 optimal weight: 0.8980 chunk 263 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 196 optimal weight: 0.0050 chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 GLN ** F 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS A 360 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.204144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154101 restraints weight = 27314.203| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.99 r_work: 0.3672 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21208 Z= 0.117 Angle : 0.499 7.177 28697 Z= 0.268 Chirality : 0.040 0.243 3119 Planarity : 0.003 0.039 3784 Dihedral : 4.253 53.885 2959 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.48 % Favored : 95.27 % Rotamer: Outliers : 3.52 % Allowed : 19.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.16), residues: 2748 helix: 1.41 (0.14), residues: 1386 sheet: -1.44 (0.29), residues: 354 loop : -0.88 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 142 TYR 0.027 0.002 TYR F 426 PHE 0.013 0.001 PHE F 166 TRP 0.009 0.001 TRP F 187 HIS 0.012 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00246 (21208) covalent geometry : angle 0.49932 (28697) hydrogen bonds : bond 0.04170 ( 1140) hydrogen bonds : angle 4.79838 ( 3372) *********************** 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 275 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 329 GLU cc_start: 0.8019 (mp0) cc_final: 0.7534 (mp0) REVERT: D 455 ASP cc_start: 0.8115 (t70) cc_final: 0.7862 (t0) REVERT: E 187 TRP cc_start: 0.7185 (p90) cc_final: 0.6474 (p90) REVERT: E 268 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6096 (t) REVERT: E 307 TRP cc_start: 0.6815 (m100) cc_final: 0.6525 (m100) REVERT: E 334 ILE cc_start: 0.7812 (mt) cc_final: 0.7568 (tt) REVERT: E 403 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6127 (tp30) REVERT: F 78 LYS cc_start: 0.7825 (tmtt) cc_final: 0.7463 (tptp) REVERT: F 354 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6501 (mp) REVERT: B 155 ILE cc_start: 0.8253 (mt) cc_final: 0.7959 (tp) REVERT: B 187 TRP cc_start: 0.7243 (p90) cc_final: 0.6722 (p90) REVERT: B 301 LEU cc_start: 0.5402 (mm) cc_final: 0.5110 (mt) REVERT: B 309 HIS cc_start: 0.3524 (p90) cc_final: 0.3323 (p-80) REVERT: B 390 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.4878 (pmm) REVERT: B 403 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5824 (tp30) REVERT: C 149 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6914 (m-30) REVERT: C 187 TRP cc_start: 0.6215 (p90) cc_final: 0.5840 (p90) REVERT: C 206 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: C 219 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5631 (m-80) REVERT: C 334 ILE cc_start: 0.7839 (mt) cc_final: 0.7602 (tt) REVERT: A 206 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6620 (mt-10) REVERT: A 219 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5373 (m-80) REVERT: A 258 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6777 (mp) outliers start: 74 outliers final: 33 residues processed: 255 average time/residue: 0.1290 time to fit residues: 54.1946 Evaluate side-chains 223 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 179 VAL 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 347 MET Chi-restraints excluded: chain F residue 354 ILE 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 321 THR Chi-restraints excluded: chain B residue 334 ILE 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 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 257 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 412 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 195 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 154 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 255 optimal weight: 0.0000 chunk 4 optimal weight: 0.9990 chunk 259 optimal weight: 0.8980 chunk 217 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 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 = 0.4411 r_free = 0.4411 target = 0.205216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157340 restraints weight = 27207.692| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.99 r_work: 0.3690 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1607 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= 0.110 Angle : 0.496 9.084 28697 Z= 0.264 Chirality : 0.040 0.150 3119 Planarity : 0.003 0.040 3784 Dihedral : 4.145 52.698 2959 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.18 % Favored : 95.60 % Rotamer: Outliers : 3.85 % Allowed : 18.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.16), residues: 2748 helix: 1.51 (0.14), residues: 1386 sheet: -1.31 (0.29), residues: 342 loop : -0.82 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 142 TYR 0.030 0.002 TYR F 77 PHE 0.012 0.001 PHE F 101 TRP 0.008 0.001 TRP F 187 HIS 0.011 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00234 (21208) covalent geometry : angle 0.49588 (28697) hydrogen bonds : bond 0.03913 ( 1140) hydrogen bonds : angle 4.66117 ( 3372) *********************** 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: 81 poor density : 191 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: D 226 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5578 (mt) REVERT: D 329 GLU cc_start: 0.8023 (mp0) cc_final: 0.7461 (mp0) REVERT: D 455 ASP cc_start: 0.8127 (t70) cc_final: 0.7884 (t0) REVERT: E 4 LEU cc_start: 0.8399 (tt) cc_final: 0.7981 (mp) REVERT: E 187 TRP cc_start: 0.7124 (p90) cc_final: 0.6413 (p90) REVERT: E 268 THR cc_start: 0.6300 (OUTLIER) cc_final: 0.6061 (t) REVERT: E 301 LEU cc_start: 0.5754 (mm) cc_final: 0.5349 (mt) REVERT: E 307 TRP cc_start: 0.6843 (m100) cc_final: 0.6606 (m100) REVERT: E 403 GLU cc_start: 0.6441 (mm-30) cc_final: 0.6104 (tp30) REVERT: F 206 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6306 (mt-10) REVERT: F 301 LEU cc_start: 0.5601 (mm) cc_final: 0.5336 (mt) REVERT: F 354 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6598 (mp) REVERT: B 155 ILE cc_start: 0.8223 (mt) cc_final: 0.7923 (tp) REVERT: B 187 TRP cc_start: 0.7202 (p90) cc_final: 0.6472 (p90) REVERT: B 301 LEU cc_start: 0.5403 (mm) cc_final: 0.5121 (mt) REVERT: B 403 GLU cc_start: 0.6266 (mm-30) cc_final: 0.6023 (tp30) REVERT: C 56 ASP cc_start: 0.8213 (m-30) cc_final: 0.7916 (m-30) REVERT: C 149 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: C 187 TRP cc_start: 0.5969 (p90) cc_final: 0.5715 (p90) REVERT: C 206 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7414 (mt-10) REVERT: C 208 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6268 (mmm) REVERT: C 219 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5521 (m-80) REVERT: A 206 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: A 219 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: A 258 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6723 (mp) outliers start: 81 outliers final: 40 residues processed: 251 average time/residue: 0.1245 time to fit residues: 51.6309 Evaluate side-chains 220 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 168 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 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 206 GLU Chi-restraints excluded: chain F residue 309 HIS Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 354 ILE 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 416 PHE Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 110 MET 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 250 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 412 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 371 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 218 optimal weight: 0.0000 chunk 40 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** B 309 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.203563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152174 restraints weight = 27096.464| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.74 r_work: 0.3673 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21208 Z= 0.141 Angle : 0.513 8.097 28697 Z= 0.274 Chirality : 0.041 0.297 3119 Planarity : 0.003 0.040 3784 Dihedral : 4.146 49.109 2959 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.73 % Favored : 95.09 % Rotamer: Outliers : 3.80 % Allowed : 19.31 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2748 helix: 1.54 (0.14), residues: 1386 sheet: -1.33 (0.29), residues: 342 loop : -0.80 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.040 0.002 TYR F 77 PHE 0.012 0.002 PHE F 132 TRP 0.008 0.001 TRP F 187 HIS 0.006 0.001 HIS F 360 Details of bonding type rmsd covalent geometry : bond 0.00320 (21208) covalent geometry : angle 0.51261 (28697) hydrogen bonds : bond 0.04128 ( 1140) hydrogen bonds : angle 4.66213 ( 3372) *********************** 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 259 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 179 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: D 226 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.5656 (mt) REVERT: D 329 GLU cc_start: 0.8065 (mp0) cc_final: 0.7493 (mp0) REVERT: E 4 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8012 (mp) REVERT: E 69 GLN cc_start: 0.8366 (mt0) cc_final: 0.8124 (mt0) REVERT: E 268 THR cc_start: 0.6284 (OUTLIER) cc_final: 0.6066 (t) REVERT: E 301 LEU cc_start: 0.5802 (mm) cc_final: 0.5417 (mt) REVERT: E 307 TRP cc_start: 0.6892 (m100) cc_final: 0.6609 (m100) REVERT: E 403 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6110 (tp30) REVERT: F 206 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6363 (mt-10) REVERT: F 301 LEU cc_start: 0.5612 (mm) cc_final: 0.5338 (mt) REVERT: F 354 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6499 (mp) REVERT: B 155 ILE cc_start: 0.8202 (mt) cc_final: 0.7944 (tp) REVERT: B 187 TRP cc_start: 0.7183 (p90) cc_final: 0.6603 (p90) REVERT: B 301 LEU cc_start: 0.5468 (mm) cc_final: 0.5112 (mt) REVERT: B 403 GLU cc_start: 0.6254 (mm-30) cc_final: 0.5921 (tp30) REVERT: C 56 ASP cc_start: 0.8175 (m-30) cc_final: 0.7861 (m-30) REVERT: C 149 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: C 187 TRP cc_start: 0.6005 (p90) cc_final: 0.5763 (p90) REVERT: C 206 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7349 (mt-10) REVERT: C 208 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6332 (mmm) REVERT: C 219 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.5369 (m-80) REVERT: A 206 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: A 219 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: A 258 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6724 (mp) outliers start: 80 outliers final: 47 residues processed: 241 average time/residue: 0.1331 time to fit residues: 53.1858 Evaluate side-chains 229 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 70 PHE Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 179 VAL 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 433 ILE 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 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 191 LEU 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 354 ILE 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 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 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 78 LYS 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 250 LEU Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 412 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 249 optimal weight: 5.9990 chunk 212 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 150 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS F 48 GLN F 71 ASN ** F 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN A 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.201727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156359 restraints weight = 27095.479| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.75 r_work: 0.3646 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1548 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= 0.177 Angle : 0.548 8.310 28697 Z= 0.293 Chirality : 0.042 0.180 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.302 44.254 2959 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.42 % Favored : 94.40 % Rotamer: Outliers : 4.42 % Allowed : 19.64 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2748 helix: 1.47 (0.14), residues: 1386 sheet: -1.47 (0.29), residues: 354 loop : -0.85 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.032 0.002 TYR F 77 PHE 0.015 0.002 PHE B 132 TRP 0.010 0.001 TRP F 187 HIS 0.005 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00412 (21208) covalent geometry : angle 0.54816 (28697) hydrogen bonds : bond 0.04475 ( 1140) hydrogen bonds : angle 4.70052 ( 3372) *********************** 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 281 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 188 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: D 219 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: D 226 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5771 (mt) REVERT: D 329 GLU cc_start: 0.8090 (mp0) cc_final: 0.7486 (mp0) REVERT: E 4 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7991 (mp) REVERT: E 268 THR cc_start: 0.6310 (OUTLIER) cc_final: 0.6096 (t) REVERT: E 307 TRP cc_start: 0.6964 (m100) cc_final: 0.6642 (m100) REVERT: E 403 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6079 (tp30) REVERT: F 78 LYS cc_start: 0.7985 (tmtt) cc_final: 0.7457 (tptp) REVERT: F 206 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6449 (mt-10) REVERT: F 298 PHE cc_start: 0.4686 (OUTLIER) cc_final: 0.2911 (m-80) REVERT: F 301 LEU cc_start: 0.5653 (mm) cc_final: 0.5342 (mt) REVERT: F 354 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6567 (mp) REVERT: B 155 ILE cc_start: 0.8235 (mt) cc_final: 0.7957 (tp) REVERT: B 187 TRP cc_start: 0.7462 (p90) cc_final: 0.6926 (p90) REVERT: B 301 LEU cc_start: 0.5735 (mm) cc_final: 0.5312 (mt) REVERT: B 307 TRP cc_start: 0.6703 (m100) cc_final: 0.6421 (m100) REVERT: B 389 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6059 (tp30) REVERT: B 403 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5874 (tp30) REVERT: B 412 MET cc_start: 0.2256 (ppp) cc_final: 0.1858 (ppp) REVERT: C 56 ASP cc_start: 0.8251 (m-30) cc_final: 0.7905 (m-30) REVERT: C 149 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: C 187 TRP cc_start: 0.6330 (p90) cc_final: 0.6074 (p90) REVERT: C 206 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: C 219 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5602 (m-80) REVERT: A 206 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: A 219 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: A 258 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6811 (mp) outliers start: 93 outliers final: 53 residues processed: 260 average time/residue: 0.1236 time to fit residues: 53.5454 Evaluate side-chains 249 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 181 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 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 106 THR 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 390 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 319 SER Chi-restraints excluded: chain F residue 347 MET Chi-restraints excluded: chain F residue 354 ILE 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 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 389 GLU Chi-restraints excluded: chain B residue 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 78 LYS 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 309 HIS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 412 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 206 GLU Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 209 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 22 optimal weight: 20.0000 chunk 255 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 235 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 223 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS E 360 HIS F 360 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 = 0.4403 r_free = 0.4403 target = 0.204267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154650 restraints weight = 27235.800| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.13 r_work: 0.3661 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21208 Z= 0.121 Angle : 0.511 8.450 28697 Z= 0.272 Chirality : 0.040 0.183 3119 Planarity : 0.003 0.041 3784 Dihedral : 3.972 34.460 2955 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.16 % Rotamer: Outliers : 3.85 % Allowed : 20.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.16), residues: 2748 helix: 1.54 (0.14), residues: 1386 sheet: -1.18 (0.29), residues: 348 loop : -0.80 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.033 0.002 TYR B 235 PHE 0.011 0.001 PHE F 101 TRP 0.008 0.001 TRP C 187 HIS 0.006 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00268 (21208) covalent geometry : angle 0.51137 (28697) hydrogen bonds : bond 0.03999 ( 1140) hydrogen bonds : angle 4.59927 ( 3372) *********************** 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 273 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 192 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: D 56 ASP cc_start: 0.8083 (m-30) cc_final: 0.7798 (m-30) REVERT: D 219 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5641 (m-80) REVERT: D 226 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5680 (mt) REVERT: D 329 GLU cc_start: 0.8086 (mp0) cc_final: 0.7522 (mp0) REVERT: E 4 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7986 (mp) REVERT: E 187 TRP cc_start: 0.7038 (p90) cc_final: 0.6620 (p90) REVERT: E 268 THR cc_start: 0.6286 (OUTLIER) cc_final: 0.6062 (t) REVERT: E 301 LEU cc_start: 0.5805 (mm) cc_final: 0.5423 (mt) REVERT: E 307 TRP cc_start: 0.6890 (m100) cc_final: 0.6609 (m100) REVERT: E 412 MET cc_start: 0.2606 (ppp) cc_final: 0.2321 (ppp) REVERT: F 78 LYS cc_start: 0.7797 (tmtt) cc_final: 0.7507 (tptp) REVERT: F 206 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6349 (mt-10) REVERT: F 298 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.2894 (m-80) REVERT: F 301 LEU cc_start: 0.5646 (mm) cc_final: 0.5362 (mt) REVERT: B 4 LEU cc_start: 0.8404 (tt) cc_final: 0.8155 (mp) REVERT: B 155 ILE cc_start: 0.8264 (mt) cc_final: 0.7946 (tp) REVERT: B 180 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7189 (pp) REVERT: B 187 TRP cc_start: 0.7341 (p90) cc_final: 0.6821 (p90) REVERT: B 301 LEU cc_start: 0.5913 (mm) cc_final: 0.5532 (mt) REVERT: B 307 TRP cc_start: 0.6568 (m100) cc_final: 0.6288 (m100) REVERT: B 309 HIS cc_start: 0.3694 (p90) cc_final: 0.3327 (p-80) REVERT: B 403 GLU cc_start: 0.6170 (mm-30) cc_final: 0.5865 (tp30) REVERT: B 412 MET cc_start: 0.2124 (ppp) cc_final: 0.1766 (ppp) REVERT: C 56 ASP cc_start: 0.8237 (m-30) cc_final: 0.7890 (m-30) REVERT: C 149 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: C 206 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: C 208 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6232 (mmm) REVERT: C 219 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5424 (m-80) REVERT: A 206 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: A 219 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5322 (m-80) REVERT: A 258 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6676 (mp) outliers start: 81 outliers final: 51 residues processed: 256 average time/residue: 0.1265 time to fit residues: 53.4737 Evaluate side-chains 236 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 78 LYS 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 108 LEU Chi-restraints excluded: chain E residue 179 VAL 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 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 180 LEU 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 416 PHE Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 106 THR 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 250 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 412 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 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 289 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 371 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 229 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 32 optimal weight: 0.0020 chunk 232 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 104 optimal weight: 0.4980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 E 109 ASN ** B 211 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.205240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.158321 restraints weight = 27006.138| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.90 r_work: 0.3679 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21208 Z= 0.115 Angle : 0.510 8.437 28697 Z= 0.271 Chirality : 0.040 0.187 3119 Planarity : 0.003 0.041 3784 Dihedral : 3.901 34.402 2955 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 3.71 % Allowed : 21.07 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.17), residues: 2748 helix: 1.54 (0.14), residues: 1392 sheet: -1.13 (0.29), residues: 348 loop : -0.74 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 142 TYR 0.019 0.002 TYR B 199 PHE 0.013 0.001 PHE C 166 TRP 0.023 0.001 TRP C 187 HIS 0.006 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00253 (21208) covalent geometry : angle 0.51018 (28697) hydrogen bonds : bond 0.03808 ( 1140) hydrogen bonds : angle 4.56687 ( 3372) *********************** 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 266 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 188 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: D 219 PHE cc_start: 0.6215 (OUTLIER) cc_final: 0.5611 (m-80) REVERT: D 226 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5775 (mt) REVERT: D 329 GLU cc_start: 0.8053 (mp0) cc_final: 0.7487 (mp0) REVERT: E 4 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7994 (mp) REVERT: E 268 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6202 (t) REVERT: E 301 LEU cc_start: 0.5859 (mm) cc_final: 0.5458 (mt) REVERT: E 307 TRP cc_start: 0.6881 (m100) cc_final: 0.6588 (m100) REVERT: E 309 HIS cc_start: 0.4186 (m90) cc_final: 0.3771 (m90) REVERT: F 98 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7235 (mm-30) REVERT: F 298 PHE cc_start: 0.4715 (OUTLIER) cc_final: 0.2998 (m-80) REVERT: F 301 LEU cc_start: 0.5819 (mm) cc_final: 0.5496 (mt) REVERT: B 4 LEU cc_start: 0.8408 (tt) cc_final: 0.8193 (mp) REVERT: B 155 ILE cc_start: 0.8211 (mt) cc_final: 0.7870 (tp) REVERT: B 187 TRP cc_start: 0.7345 (p90) cc_final: 0.6798 (p90) REVERT: B 301 LEU cc_start: 0.6087 (mm) cc_final: 0.5725 (mt) REVERT: B 307 TRP cc_start: 0.6523 (m100) cc_final: 0.6238 (m100) REVERT: B 309 HIS cc_start: 0.3615 (p90) cc_final: 0.3298 (p-80) REVERT: B 412 MET cc_start: 0.2135 (ppp) cc_final: 0.1809 (ppp) REVERT: C 56 ASP cc_start: 0.8120 (m-30) cc_final: 0.7765 (m-30) REVERT: C 149 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: C 208 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6121 (mmm) REVERT: C 219 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5378 (m-80) REVERT: A 187 TRP cc_start: 0.6931 (p90) cc_final: 0.6718 (p90) REVERT: A 206 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6757 (mt-10) REVERT: A 219 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5248 (m-80) REVERT: A 258 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6763 (mp) outliers start: 78 outliers final: 49 residues processed: 251 average time/residue: 0.1375 time to fit residues: 56.6309 Evaluate side-chains 239 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 191 LEU 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 416 PHE Chi-restraints excluded: chain B residue 437 LEU 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 149 ASP 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 347 MET Chi-restraints excluded: chain C residue 412 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 70 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 100 optimal weight: 0.0020 chunk 37 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 45 optimal weight: 0.0170 chunk 236 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 overall best weight: 1.3230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** B 211 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.203697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152093 restraints weight = 27203.486| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.06 r_work: 0.3654 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21208 Z= 0.141 Angle : 0.540 8.226 28697 Z= 0.288 Chirality : 0.041 0.182 3119 Planarity : 0.003 0.040 3784 Dihedral : 3.951 34.837 2955 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.88 % Favored : 94.94 % Rotamer: Outliers : 3.42 % Allowed : 21.30 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2748 helix: 1.53 (0.14), residues: 1386 sheet: -1.19 (0.29), residues: 348 loop : -0.75 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 142 TYR 0.023 0.002 TYR F 77 PHE 0.016 0.002 PHE C 166 TRP 0.023 0.001 TRP C 187 HIS 0.021 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00323 (21208) covalent geometry : angle 0.54014 (28697) hydrogen bonds : bond 0.04042 ( 1140) hydrogen bonds : angle 4.61856 ( 3372) *********************** 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: 72 poor density : 184 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: D 219 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5505 (m-80) REVERT: D 226 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5791 (mt) REVERT: D 329 GLU cc_start: 0.8041 (mp0) cc_final: 0.7455 (mp0) REVERT: E 4 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7988 (mp) REVERT: E 268 THR cc_start: 0.6311 (OUTLIER) cc_final: 0.6093 (t) REVERT: E 301 LEU cc_start: 0.5803 (mm) cc_final: 0.5356 (mt) REVERT: E 307 TRP cc_start: 0.6944 (m100) cc_final: 0.6652 (m100) REVERT: E 309 HIS cc_start: 0.4217 (m90) cc_final: 0.3785 (m90) REVERT: F 98 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7292 (mm-30) REVERT: F 298 PHE cc_start: 0.4701 (OUTLIER) cc_final: 0.2968 (m-80) REVERT: F 301 LEU cc_start: 0.5921 (mm) cc_final: 0.5586 (mt) REVERT: B 4 LEU cc_start: 0.8408 (tt) cc_final: 0.8191 (mp) REVERT: B 40 VAL cc_start: 0.8906 (t) cc_final: 0.8610 (m) REVERT: B 155 ILE cc_start: 0.8241 (mt) cc_final: 0.7944 (tp) REVERT: B 180 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7076 (pp) REVERT: B 187 TRP cc_start: 0.7398 (p90) cc_final: 0.6874 (p90) REVERT: B 301 LEU cc_start: 0.5988 (mm) cc_final: 0.5568 (mt) REVERT: B 307 TRP cc_start: 0.6542 (m100) cc_final: 0.6265 (m100) REVERT: B 309 HIS cc_start: 0.3666 (p90) cc_final: 0.3357 (p-80) REVERT: B 412 MET cc_start: 0.1843 (ppp) cc_final: 0.1566 (ppp) REVERT: C 56 ASP cc_start: 0.8210 (m-30) cc_final: 0.7844 (m-30) REVERT: C 149 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: C 208 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6152 (mmm) REVERT: C 219 PHE cc_start: 0.6316 (OUTLIER) cc_final: 0.5394 (m-80) REVERT: C 329 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7367 (pt0) REVERT: A 206 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: A 219 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5293 (m-80) REVERT: A 258 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6826 (mp) outliers start: 72 outliers final: 53 residues processed: 239 average time/residue: 0.1317 time to fit residues: 52.1658 Evaluate side-chains 241 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 175 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 347 MET 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 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 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 298 PHE 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 180 LEU 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 416 PHE Chi-restraints excluded: chain B residue 437 LEU 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 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 412 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 151 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 B 109 ASN ** B 211 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.202142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151301 restraints weight = 27175.732| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.87 r_work: 0.3647 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1907 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= 0.174 Angle : 0.573 8.520 28697 Z= 0.306 Chirality : 0.042 0.175 3119 Planarity : 0.004 0.040 3784 Dihedral : 4.104 36.245 2955 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.99 % Favored : 94.83 % Rotamer: Outliers : 3.38 % Allowed : 21.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.17), residues: 2748 helix: 1.26 (0.14), residues: 1428 sheet: -1.23 (0.29), residues: 348 loop : -0.90 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 142 TYR 0.031 0.002 TYR B 235 PHE 0.020 0.002 PHE E 94 TRP 0.026 0.002 TRP C 187 HIS 0.016 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00405 (21208) covalent geometry : angle 0.57327 (28697) hydrogen bonds : bond 0.04362 ( 1140) hydrogen bonds : angle 4.68257 ( 3372) ********************** 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 247 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 16 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: D 219 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5618 (m-80) REVERT: D 226 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5781 (mt) REVERT: D 329 GLU cc_start: 0.8078 (mp0) cc_final: 0.7459 (mp0) REVERT: E 4 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7987 (mp) REVERT: E 268 THR cc_start: 0.6319 (OUTLIER) cc_final: 0.6099 (t) REVERT: E 301 LEU cc_start: 0.5833 (mm) cc_final: 0.5388 (mt) REVERT: E 307 TRP cc_start: 0.6975 (m100) cc_final: 0.6629 (m100) REVERT: E 309 HIS cc_start: 0.4252 (m90) cc_final: 0.3849 (m90) REVERT: F 34 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7900 (mtp180) REVERT: F 78 LYS cc_start: 0.7883 (tmtt) cc_final: 0.7526 (tptp) REVERT: F 98 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7292 (mm-30) REVERT: F 298 PHE cc_start: 0.4715 (OUTLIER) cc_final: 0.2908 (m-80) REVERT: F 301 LEU cc_start: 0.5862 (mm) cc_final: 0.5507 (mt) REVERT: B 4 LEU cc_start: 0.8413 (tt) cc_final: 0.8197 (mp) REVERT: B 155 ILE cc_start: 0.8257 (mt) cc_final: 0.7992 (tp) REVERT: B 180 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7144 (pp) REVERT: B 187 TRP cc_start: 0.7446 (p90) cc_final: 0.6871 (p90) REVERT: B 301 LEU cc_start: 0.5904 (mm) cc_final: 0.5449 (mt) REVERT: B 307 TRP cc_start: 0.6604 (m100) cc_final: 0.6342 (m100) REVERT: B 412 MET cc_start: 0.1954 (ppp) cc_final: 0.1662 (ppp) REVERT: C 56 ASP cc_start: 0.8209 (m-30) cc_final: 0.7850 (m-30) REVERT: C 109 ASN cc_start: 0.6105 (OUTLIER) cc_final: 0.5271 (p0) REVERT: C 208 MET cc_start: 0.6589 (OUTLIER) cc_final: 0.6126 (mmm) REVERT: C 219 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5385 (m-80) REVERT: C 242 GLU cc_start: 0.3016 (mt-10) cc_final: 0.2769 (mt-10) REVERT: A 206 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: A 219 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: A 258 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6815 (mp) outliers start: 71 outliers final: 51 residues processed: 230 average time/residue: 0.1309 time to fit residues: 50.3147 Evaluate side-chains 234 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 347 MET 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 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 108 LEU 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 390 MET 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 298 PHE 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 180 LEU 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 416 PHE Chi-restraints excluded: chain B residue 437 LEU 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 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 412 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 229 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 235 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 233 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 360 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151109 restraints weight = 27017.001| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.05 r_work: 0.3638 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 21208 Z= 0.168 Angle : 0.727 59.200 28697 Z= 0.419 Chirality : 0.042 0.348 3119 Planarity : 0.004 0.068 3784 Dihedral : 4.102 36.240 2955 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.91 % Favored : 94.91 % Rotamer: Outliers : 3.23 % Allowed : 21.59 % Favored : 75.18 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.17), residues: 2748 helix: 1.27 (0.14), residues: 1428 sheet: -1.23 (0.29), residues: 348 loop : -0.89 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.023 0.002 TYR F 235 PHE 0.018 0.002 PHE E 94 TRP 0.030 0.001 TRP C 187 HIS 0.016 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00364 (21208) covalent geometry : angle 0.72659 (28697) hydrogen bonds : bond 0.04306 ( 1140) hydrogen bonds : angle 4.68300 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6635.52 seconds wall clock time: 114 minutes 0.51 seconds (6840.51 seconds total)