Starting phenix.real_space_refine
on Thu Sep 18 03:37:29 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/9g75_51110/09_2025/9g75_51110.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g75_51110/09_2025/9g75_51110.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g75_51110/09_2025/9g75_51110.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g75_51110/09_2025/9g75_51110.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g75_51110/09_2025/9g75_51110.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g75_51110/09_2025/9g75_51110.map"
  }
  resolution = 2.98
  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=   0.972
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: 5
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     S      72      5.16       5
     C    8655      2.51       5
     N    2411      2.21       5
     O    2604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  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: 13780
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 850, 6755
          Classifications: {'peptide': 850}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 60, 'TRANS': 789}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2, 'TRP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 3127
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3127
          Classifications: {'peptide': 393}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 374}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 3118
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 391, 3108
          Classifications: {'peptide': 391}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
      Conformer: "B"
        Number of residues, atoms: 391, 3108
          Classifications: {'peptide': 391}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 372}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
          bond proxies already assigned to first conformer: 3169
    Chain: "P"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 397
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "T"
      Number of atoms: 383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 383
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS C 161 " occ=0.69
      ... (18 atoms not shown)
      pdb=" NE2BHIS C 161 " occ=0.31
  Time building chain proxies: 3.80, per 1000 atoms: 0.28
  Number of scatterers: 13780
  At special positions: 0
  Unit cell: (100.65, 103.125, 145.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     P      38     15.00
     O    2604      8.00
     N    2411      7.00
     C    8655      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: 1.28
  Conformation dependent library (CDL) restraints added in 662.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3066

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 15 sheets defined
      47.3% alpha, 14.3% beta
      19 base pairs and 33 stacking pairs defined.
    Time for finding SS restraints: 1.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 71
      removed outlier: 3.636A  pdb=" N   GLN A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 94
    Processing helix  chain 'A' and resid 117 through 130
    Processing helix  chain 'A' and resid 130 through 142
      removed outlier: 3.752A  pdb=" N   LEU A 140 " --> pdb=" O   ALA A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.542A  pdb=" N   VAL A 212 " --> pdb=" O   SER A 208 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLU A 214 " --> pdb=" O   ARG A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 227
      removed outlier: 3.693A  pdb=" N   LEU A 227 " --> pdb=" O   PRO A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 260
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 3.593A  pdb=" N   GLN A 264 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   TYR A 265 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LEU A 266 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 261 through 266'
    Processing helix  chain 'A' and resid 277 through 286
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.753A  pdb=" N   SER A 293 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 332
      removed outlier: 3.503A  pdb=" N   ASP A 331 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 346
    Processing helix  chain 'A' and resid 363 through 370
    Processing helix  chain 'A' and resid 370 through 400
      removed outlier: 4.071A  pdb=" N   GLN A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ASP A 381 " --> pdb=" O   TYR A 377 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLN A 391 " --> pdb=" O   GLU A 387 " (cutoff:3.500A)
      Proline residue:  A 394  - end of helix
    Processing helix  chain 'A' and resid 402 through 413
      removed outlier: 4.057A  pdb=" N   LEU A 406 " --> pdb=" O   HIS A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 451
      removed outlier: 3.642A  pdb=" N   ARG A 425 " --> pdb=" O   GLN A 421 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A 448 " --> pdb=" O   SER A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 459 through 464
      removed outlier: 3.919A  pdb=" N   LYS A 462 " --> pdb=" O   GLU A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 532
      removed outlier: 3.745A  pdb=" N   LEU A 520 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU A 530 " --> pdb=" O   ALA A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 540
      removed outlier: 3.654A  pdb=" N   THR A 537 " --> pdb=" O   ARG A 534 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   ASP A 538 " --> pdb=" O   SER A 535 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU A 540 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 558
      removed outlier: 3.509A  pdb=" N   LEU A 557 " --> pdb=" O   TRP A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 584
    Processing helix  chain 'A' and resid 629 through 640
    Processing helix  chain 'A' and resid 745 through 747
      No H-bonds generated for 'chain 'A' and resid 745 through 747'
    Processing helix  chain 'A' and resid 748 through 754
    Processing helix  chain 'A' and resid 766 through 787
      removed outlier: 3.586A  pdb=" N   LEU A 770 " --> pdb=" O   GLY A 766 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   PHE A 778 " --> pdb=" O   LYS A 774 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   TRP A 779 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   LYS A 784 " --> pdb=" O   ARG A 780 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   ARG A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 849 through 856
      removed outlier: 4.582A  pdb=" N   LYS A 853 " --> pdb=" O   SER A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 885
      removed outlier: 3.547A  pdb=" N   HIS A 884 " --> pdb=" O   LEU A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 900
      removed outlier: 3.742A  pdb=" N   GLN A 900 " --> pdb=" O   TRP A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1044
    Processing helix  chain 'A' and resid 1070 through 1101
      removed outlier: 3.803A  pdb=" N   VAL A1079 " --> pdb=" O   VAL A1075 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1146
      removed outlier: 3.702A  pdb=" N   LEU A1146 " --> pdb=" O   PHE A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1182 through 1188
      removed outlier: 3.900A  pdb=" N   ARG A1186 " --> pdb=" O   THR A1182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1197 through 1206
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 61 through 68
      removed outlier: 3.595A  pdb=" N   GLY B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 93
      removed outlier: 3.703A  pdb=" N   GLU B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 133
    Processing helix  chain 'B' and resid 137 through 152
      removed outlier: 3.960A  pdb=" N   VAL B 142 " --> pdb=" O   LYS B 138 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA B 143 " --> pdb=" O   GLU B 139 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE B 144 " --> pdb=" O   GLN B 140 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B 149 " --> pdb=" O   LEU B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 166
    Processing helix  chain 'B' and resid 166 through 174
      removed outlier: 3.677A  pdb=" N   ASP B 172 " --> pdb=" O   VAL B 168 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU B 173 " --> pdb=" O   ASN B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 241
      removed outlier: 4.644A  pdb=" N   SER B 223 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   GLN B 224 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   PHE B 240 " --> pdb=" O   TRP B 236 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA B 241 " --> pdb=" O   TRP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 245
      No H-bonds generated for 'chain 'B' and resid 243 through 245'
    Processing helix  chain 'B' and resid 282 through 289
    Processing helix  chain 'B' and resid 292 through 296
    Processing helix  chain 'B' and resid 316 through 328
      removed outlier: 3.606A  pdb=" N   LEU B 321 " --> pdb=" O   ASP B 317 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE B 328 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 365 through 382
    Processing helix  chain 'B' and resid 391 through 393
      No H-bonds generated for 'chain 'B' and resid 391 through 393'
    Processing helix  chain 'B' and resid 398 through 409
    Processing helix  chain 'B' and resid 418 through 423
    Processing helix  chain 'B' and resid 444 through 457
      removed outlier: 3.519A  pdb=" N   SER B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 56 through 60
      removed outlier: 3.512A  pdb=" N   LEU C  60 " --> pdb=" O   PRO C  57 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 68
      removed outlier: 3.524A  pdb=" N   GLY C  68 " --> pdb=" O   ALA C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 93
      removed outlier: 3.747A  pdb=" N   GLU C  79 " --> pdb=" O   PRO C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 133
    Processing helix  chain 'C' and resid 137 through 151
      removed outlier: 3.655A  pdb=" N   LEU C 149 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 165
    Processing helix  chain 'C' and resid 166 through 174
      removed outlier: 3.744A  pdb=" N   VAL C 174 " --> pdb=" O   CYS C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 241
      removed outlier: 3.992A  pdb=" N   PHE C 240 " --> pdb=" O   TRP C 236 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ALA C 241 " --> pdb=" O   TRP C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 245
      No H-bonds generated for 'chain 'C' and resid 243 through 245'
    Processing helix  chain 'C' and resid 282 through 289
    Processing helix  chain 'C' and resid 316 through 328
    Processing helix  chain 'C' and resid 365 through 383
    Processing helix  chain 'C' and resid 391 through 393
      No H-bonds generated for 'chain 'C' and resid 391 through 393'
    Processing helix  chain 'C' and resid 398 through 408
    Processing helix  chain 'C' and resid 418 through 424
      removed outlier: 3.976A  pdb=" N   LEU C 422 " --> pdb=" O   THR C 418 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 458
      removed outlier: 4.363A  pdb=" N   ARG C 446 " --> pdb=" O   ILE C 442 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ASP C 447 " --> pdb=" O   SER C 443 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 161
      removed outlier: 3.582A  pdb=" N   GLY A 157 " --> pdb=" O   CYS A 207 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   CYS A 207 " --> pdb=" O   GLY A 157 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   TRP A 203 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   GLN A 247 " --> pdb=" O   ARG A 273 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU A 275 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 419
      removed outlier: 4.239A  pdb=" N   TYR A 815 " --> pdb=" O   LEU A 794 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 587 through 588
    Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1105 through 1109
      removed outlier: 7.000A  pdb=" N   ARG A1116 " --> pdb=" O   CYS A1108 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU A1196 " --> pdb=" O   VAL A1161 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 101
      removed outlier: 5.877A  pdb=" N   PHE B 100 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   ILE B 185 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   VAL B 309 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   THR B 276 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ILE B 274 " --> pdb=" O   ASP B 315 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   TYR B 265 " --> pdb=" O   PRO B 273 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLU B 275 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LYS B 259 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108
    Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122
    Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 299
    Processing sheet with id=AB1, first strand: chain 'B' and resid 357 through 359
      removed outlier: 6.797A  pdb=" N   VAL B 357 " --> pdb=" O   TRP B 388 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 413 through 416
      removed outlier: 3.644A  pdb=" N   ARG B 430 " --> pdb=" O   SER B 414 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 99 through 101
      removed outlier: 6.201A  pdb=" N   PHE C 100 " --> pdb=" O   ALA C 183 " (cutoff:3.500A)
      removed outlier: 8.443A  pdb=" N   ILE C 185 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   VAL C 309 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ILE C 274 " --> pdb=" O   ASP C 315 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   LYS C 271 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   PHE C 267 " --> pdb=" O   LYS C 271 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   TYR C 265 " --> pdb=" O   PRO C 273 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   LYS C 259 " --> pdb=" O   ASN C 279 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 107 through 108
    Processing sheet with id=AB5, first strand: chain 'C' and resid 298 through 299
    Processing sheet with id=AB6, first strand: chain 'C' and resid 387 through 389
      removed outlier: 7.201A  pdb=" N   TRP C 388 " --> pdb=" O   ILE C 355 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   VAL C 357 " --> pdb=" O   TRP C 388 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LYS C 356 " --> pdb=" O   PHE C 413 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   VAL C 415 " --> pdb=" O   LYS C 356 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   ALA C 358 " --> pdb=" O   VAL C 415 " (cutoff:3.500A)
      removed outlier: 7.174A  pdb=" N   VAL C 417 " --> pdb=" O   ALA C 358 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   ASP C 360 " --> pdb=" O   VAL C 417 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN C 428 " --> pdb=" O   LEU C 416 " (cutoff:3.500A)

    603 hydrogen bonds defined for protein.
    1701 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      49 hydrogen bonds
      94 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      33 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 1.68 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 3902
        1.33 -     1.45: 2562
        1.45 -     1.57: 7547
        1.57 -     1.69: 74
        1.69 -     1.81: 112
  Bond restraints: 14197
  Sorted by residual:
  bond pdb=" CA  SER B  54 "
       pdb=" C   SER B  54 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.031 1.22e-02 6.72e+03 6.44e+00
  bond pdb=" CA  ASN A 253 "
       pdb=" C   ASN A 253 "
    ideal  model  delta    sigma   weight residual
    1.531  1.498  0.033 1.46e-02 4.69e+03 5.13e+00
  bond pdb=" CA  VAL B 312 "
       pdb=" C   VAL B 312 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.28e-02 6.10e+03 4.97e+00
  bond pdb=" CA  SER C 431 "
       pdb=" C   SER C 431 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 1.24e-02 6.50e+03 4.58e+00
  bond pdb=" CA  GLY B 314 "
       pdb=" C   GLY B 314 "
    ideal  model  delta    sigma   weight residual
    1.516  1.494  0.022 1.07e-02 8.73e+03 4.42e+00
  ... (remaining 14192 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 19143
        1.89 -     3.77: 264
        3.77 -     5.66: 20
        5.66 -     7.54: 1
        7.54 -     9.43: 1
  Bond angle restraints: 19429
  Sorted by residual:
  angle pdb=" N   SER B 313 "
        pdb=" CA  SER B 313 "
        pdb=" C   SER B 313 "
      ideal   model   delta    sigma   weight residual
     107.67  117.10   -9.43 2.09e+00 2.29e-01 2.04e+01
  angle pdb=" N   VAL C 345 "
        pdb=" CA  VAL C 345 "
        pdb=" C   VAL C 345 "
      ideal   model   delta    sigma   weight residual
     107.77  113.77   -6.00 1.48e+00 4.57e-01 1.65e+01
  angle pdb=" N   VAL B 312 "
        pdb=" CA  VAL B 312 "
        pdb=" C   VAL B 312 "
      ideal   model   delta    sigma   weight residual
     107.80  102.31    5.49 1.45e+00 4.76e-01 1.44e+01
  angle pdb=" C   SER B 313 "
        pdb=" CA  SER B 313 "
        pdb=" CB  SER B 313 "
      ideal   model   delta    sigma   weight residual
     112.09  107.30    4.79 1.43e+00 4.89e-01 1.12e+01
  angle pdb=" N   ILE C 296 "
        pdb=" CA  ILE C 296 "
        pdb=" C   ILE C 296 "
      ideal   model   delta    sigma   weight residual
     112.96  109.75    3.21 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 19424 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.70: 8188
       35.70 -    71.39: 177
       71.39 -   107.09: 1
      107.09 -   142.78: 0
      142.78 -   178.48: 2
  Dihedral angle restraints: 8368
    sinusoidal: 3639
      harmonic: 4729
  Sorted by residual:
  dihedral pdb=" C4'  DG T  31 "
           pdb=" C3'  DG T  31 "
           pdb=" O3'  DG T  31 "
           pdb=" P    DA T  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.48 -178.48     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG P   8 "
           pdb=" C3'  DG P   8 "
           pdb=" O3'  DG P   8 "
           pdb=" P    DT P   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.77  155.23     1      3.50e+01 8.16e-04 1.50e+01
  dihedral pdb=" CA  HIS C  51 "
           pdb=" C   HIS C  51 "
           pdb=" N   PHE C  52 "
           pdb=" CA  PHE C  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.94   17.06     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 8365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1709
       0.044 -    0.088: 310
       0.088 -    0.132: 113
       0.132 -    0.176: 1
       0.176 -    0.219: 1
  Chirality restraints: 2134
  Sorted by residual:
  chirality pdb=" CA  VAL B 312 "
            pdb=" N   VAL B 312 "
            pdb=" C   VAL B 312 "
            pdb=" CB  VAL B 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  ILE A 198 "
            pdb=" N   ILE A 198 "
            pdb=" C   ILE A 198 "
            pdb=" CB  ILE A 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  chirality pdb=" CA  ILE A 722 "
            pdb=" N   ILE A 722 "
            pdb=" C   ILE A 722 "
            pdb=" CB  ILE A 722 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  ... (remaining 2131 not shown)

  Planarity restraints: 2362
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1177 "    0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO A1178 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A1178 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A1178 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B  53 "    0.006 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   PHE B  53 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   PHE B  53 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER B  54 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 806 "   -0.021 5.00e-02 4.00e+02   3.16e-02 1.59e+00
        pdb=" N   PRO A 807 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 807 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 807 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 2359 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1315
        2.74 -     3.28: 13466
        3.28 -     3.82: 23163
        3.82 -     4.36: 28523
        4.36 -     4.90: 47975
  Nonbonded interactions: 114442
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  63 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   LEU C 148 "
            pdb=" OG  SER C 152 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   LEU B  65 "
            pdb=" NH1 ARG B  72 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" O   GLY B 162 "
            pdb=" ND1 HIS B 166 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" O   ASN A 773 "
            pdb=" OG  SER A 777 "
     model   vdw
     2.246 3.040
  ... (remaining 114437 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 42 through 160 or resid 162 through 192 or resid 204 throu \ 
gh 328 or resid 344 through 457))
  selection = (chain 'C' and (resid 42 through 160 or resid 162 through 457))
}

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=0.31 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:             2.090
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.600
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
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      :  0.003   0.037  14197  Z= 0.158
  Angle     :  0.521   9.429  19429  Z= 0.305
  Chirality :  0.038   0.219   2134
  Planarity :  0.004   0.038   2362
  Dihedral  : 13.133 178.481   5302
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  4.08 %
    Favored  : 95.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.13 (0.21), residues: 1603
  helix:  0.22 (0.20), residues: 671
  sheet: -0.13 (0.33), residues: 245
  loop :  0.27 (0.24), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1124 
 TYR   0.010   0.001   TYR B 167 
 PHE   0.011   0.001   PHE A1158 
 TRP   0.009   0.001   TRP A 203 
 HIS   0.003   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (14197)
  covalent geometry    : angle       0.52075 (19429)
  hydrogen bonds       : bond        0.22743 (  652)
  hydrogen bonds       : angle       7.93604 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 291
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ASP cc_start: 0.6739 (m-30) cc_final: 0.6319 (m-30)
REVERT: A  476 GLU cc_start: 0.6187 (mp0) cc_final: 0.5572 (tm-30)
REVERT: A  508 GLN cc_start: 0.5482 (tp40) cc_final: 0.5129 (pp30)
REVERT: A  562 ASP cc_start: 0.7833 (m-30) cc_final: 0.7626 (m-30)
REVERT: A  836 THR cc_start: 0.6899 (m) cc_final: 0.6422 (p)
REVERT: A  897 MET cc_start: 0.6416 (ttm) cc_final: 0.6062 (tmt)
REVERT: A 1176 LYS cc_start: 0.7195 (mttp) cc_final: 0.6412 (tptt)
REVERT: A 1199 TYR cc_start: 0.6428 (m-80) cc_final: 0.6014 (m-80)
REVERT: B  399 LEU cc_start: 0.6497 (mt) cc_final: 0.5813 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 295
  average time/residue: 0.5688
  time to fit residues: 183.2613
Evaluate side-chains
  181 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  747 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A  60 GLN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 758 GLN
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  51 HIS
B 378 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5049 r_free = 0.5049 target = 0.257112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.213062 restraints weight = 20811.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.4690 rms_B_bonded: 2.40
r_work: 0.4496 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4552
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4552 r_free = 0.4552    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4552 r_free = 0.4552    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4552
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14197  Z= 0.151
  Angle     :  0.575   8.878  19429  Z= 0.298
  Chirality :  0.042   0.156   2134
  Planarity :  0.005   0.041   2362
  Dihedral  : 14.842 177.226   2168
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 11.96 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.43 (0.21), residues: 1603
  helix:  0.63 (0.19), residues: 707
  sheet:  0.00 (0.34), residues: 231
  loop :  0.22 (0.24), residues: 665

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 830 
 TYR   0.017   0.002   TYR A 461 
 PHE   0.019   0.002   PHE A 290 
 TRP   0.032   0.001   TRP C 215 
 HIS   0.006   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (14197)
  covalent geometry    : angle       0.57505 (19429)
  hydrogen bonds       : bond        0.04565 (  652)
  hydrogen bonds       : angle       5.40298 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 209
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.4922 (tt)
REVERT: A  340 ASP cc_start: 0.6772 (m-30) cc_final: 0.6346 (m-30)
REVERT: A  476 GLU cc_start: 0.6291 (mp0) cc_final: 0.5523 (tm-30)
REVERT: A  508 GLN cc_start: 0.5397 (tp40) cc_final: 0.5083 (pp30)
REVERT: A  562 ASP cc_start: 0.7814 (m-30) cc_final: 0.7586 (m-30)
REVERT: A  768 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.4091 (ttt90)
REVERT: A  801 ARG cc_start: 0.6368 (mmt180) cc_final: 0.6070 (mmm160)
REVERT: A  897 MET cc_start: 0.6751 (ttm) cc_final: 0.5971 (tmt)
REVERT: A 1094 MET cc_start: 0.6166 (OUTLIER) cc_final: 0.5535 (mmt)
REVERT: A 1116 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5433 (mtt180)
REVERT: A 1176 LYS cc_start: 0.7279 (mttp) cc_final: 0.6303 (tptt)
REVERT: B  177 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7558 (mtpp)
REVERT: C  125 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6999 (mt-10)
  outliers start: 55
  outliers final: 17
  residues processed: 244
  average time/residue: 0.4889
  time to fit residues: 132.8521
Evaluate side-chains
  198 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 VAL
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  272 MET
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  768 ARG
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue 1040 GLU
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1116 ARG
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 14 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0170
   chunk 5 optimal weight:    8.9990
   chunk 122 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 102 optimal weight:    0.7980
   chunk 56 optimal weight:    4.9990
   chunk 104 optimal weight:    4.9990
   overall best weight:    0.7020

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  55 ASN
A  60 GLN
A 117 ASN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 GLN
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 371 GLN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5060 r_free = 0.5060 target = 0.258572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.215207 restraints weight = 18203.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.4707 rms_B_bonded: 2.31
r_work: 0.4524 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4565
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4565 r_free = 0.4565    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4565 r_free = 0.4565    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14197  Z= 0.128
  Angle     :  0.541   8.886  19429  Z= 0.278
  Chirality :  0.041   0.151   2134
  Planarity :  0.004   0.043   2362
  Dihedral  : 14.785 177.824   2166
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 14.07 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.61 (0.21), residues: 1603
  helix:  0.90 (0.20), residues: 712
  sheet: -0.19 (0.33), residues: 238
  loop :  0.28 (0.24), residues: 653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 830 
 TYR   0.013   0.001   TYR A 133 
 PHE   0.030   0.002   PHE C 216 
 TRP   0.027   0.001   TRP C 215 
 HIS   0.008   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (14197)
  covalent geometry    : angle       0.54058 (19429)
  hydrogen bonds       : bond        0.03937 (  652)
  hydrogen bonds       : angle       4.99831 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 191
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  340 ASP cc_start: 0.6771 (m-30) cc_final: 0.6299 (m-30)
REVERT: A  476 GLU cc_start: 0.6251 (mp0) cc_final: 0.5499 (tm-30)
REVERT: A  508 GLN cc_start: 0.5406 (tp40) cc_final: 0.5094 (pp30)
REVERT: A  562 ASP cc_start: 0.7820 (m-30) cc_final: 0.7606 (m-30)
REVERT: A  801 ARG cc_start: 0.6335 (mmt180) cc_final: 0.6002 (mmm160)
REVERT: A  897 MET cc_start: 0.6597 (ttm) cc_final: 0.5837 (tmt)
REVERT: A 1094 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5519 (mmt)
REVERT: A 1116 ARG cc_start: 0.6048 (OUTLIER) cc_final: 0.5838 (mmp80)
REVERT: A 1176 LYS cc_start: 0.7225 (mttp) cc_final: 0.6244 (tmtt)
REVERT: A 1204 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6416 (mp)
REVERT: B  370 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.5844 (mtp180)
REVERT: C  125 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6983 (mt-10)
REVERT: C  176 ARG cc_start: 0.6924 (mtt180) cc_final: 0.5849 (mtp-110)
  outliers start: 42
  outliers final: 17
  residues processed: 215
  average time/residue: 0.5144
  time to fit residues: 122.8966
Evaluate side-chains
  195 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  747 ASP
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  828 ILE
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1116 ARG
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain A residue 1198 ILE
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   chunk 94 optimal weight:    8.9990
   chunk 105 optimal weight:    4.9990
   chunk 114 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 135 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1180 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5056 r_free = 0.5056 target = 0.258012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.214001 restraints weight = 26304.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.4702 rms_B_bonded: 2.99
r_work: 0.4452 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.4452
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4497
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4497 r_free = 0.4497    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4497 r_free = 0.4497    target_work(ls_wunit_k1) = 0.191         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4497
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  14197  Z= 0.235
  Angle     :  0.641   7.170  19429  Z= 0.330
  Chirality :  0.045   0.170   2134
  Planarity :  0.005   0.061   2362
  Dihedral  : 14.966 177.493   2166
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 15.20 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.12 (0.20), residues: 1603
  helix:  0.63 (0.19), residues: 707
  sheet: -0.46 (0.32), residues: 224
  loop : -0.16 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 432 
 TYR   0.017   0.002   TYR B 264 
 PHE   0.023   0.002   PHE C 216 
 TRP   0.024   0.002   TRP C 236 
 HIS   0.008   0.002   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00560 (14197)
  covalent geometry    : angle       0.64064 (19429)
  hydrogen bonds       : bond        0.04419 (  652)
  hydrogen bonds       : angle       5.26452 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 171
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.5026 (tt)
REVERT: A  340 ASP cc_start: 0.6886 (m-30) cc_final: 0.6405 (m-30)
REVERT: A  425 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7102 (mmm160)
REVERT: A  476 GLU cc_start: 0.6235 (mp0) cc_final: 0.5440 (tm-30)
REVERT: A  508 GLN cc_start: 0.5319 (tp40) cc_final: 0.4991 (pp30)
REVERT: A  562 ASP cc_start: 0.7821 (m-30) cc_final: 0.7565 (m-30)
REVERT: A  897 MET cc_start: 0.6633 (ttm) cc_final: 0.5867 (tmt)
REVERT: A 1034 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7144 (mp0)
REVERT: A 1094 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5575 (mmt)
REVERT: A 1204 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6435 (mp)
REVERT: B  296 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6217 (mt)
REVERT: B  310 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8264 (mt)
REVERT: B  320 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7408 (p)
REVERT: B  399 LEU cc_start: 0.6214 (mt) cc_final: 0.5780 (mt)
REVERT: C  125 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6913 (mt-10)
REVERT: C  176 ARG cc_start: 0.6896 (mtt180) cc_final: 0.5776 (mtp-110)
  outliers start: 58
  outliers final: 24
  residues processed: 206
  average time/residue: 0.5352
  time to fit residues: 121.8641
Evaluate side-chains
  192 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  425 ARG
Chi-restraints excluded: chain A residue  469 ASP
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  747 ASP
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain A residue 1204 LEU
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  296 ILE
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  320 THR
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 7 optimal weight:    0.0870
   chunk 15 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 132 optimal weight:    0.6980
   chunk 113 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 161 optimal weight:    0.6980
   chunk 5 optimal weight:   10.0000
   chunk 156 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.6158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5100 r_free = 0.5100 target = 0.263368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4777 r_free = 0.4777 target = 0.218149 restraints weight = 26559.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.4741 rms_B_bonded: 3.06
r_work: 0.4485 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.4485
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4540 r_free = 0.4540    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4540 r_free = 0.4540    target_work(ls_wunit_k1) = 0.195         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14197  Z= 0.123
  Angle     :  0.542   8.586  19429  Z= 0.279
  Chirality :  0.040   0.150   2134
  Planarity :  0.004   0.046   2362
  Dihedral  : 14.820 178.282   2166
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.31 %
    Favored  : 80.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.21), residues: 1603
  helix:  0.94 (0.20), residues: 712
  sheet: -0.41 (0.33), residues: 219
  loop :  0.04 (0.24), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 830 
 TYR   0.012   0.001   TYR A 133 
 PHE   0.024   0.001   PHE C 216 
 TRP   0.029   0.001   TRP C 215 
 HIS   0.008   0.001   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (14197)
  covalent geometry    : angle       0.54177 (19429)
  hydrogen bonds       : bond        0.03605 (  652)
  hydrogen bonds       : angle       4.85321 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 177
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5008 (tt)
REVERT: A  340 ASP cc_start: 0.6820 (m-30) cc_final: 0.6312 (m-30)
REVERT: A  476 GLU cc_start: 0.6108 (mp0) cc_final: 0.5284 (tm-30)
REVERT: A  508 GLN cc_start: 0.5142 (tp40) cc_final: 0.4924 (pp30)
REVERT: A  897 MET cc_start: 0.6651 (ttm) cc_final: 0.5871 (tmt)
REVERT: A 1094 MET cc_start: 0.6173 (OUTLIER) cc_final: 0.5671 (mmt)
REVERT: B  310 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8196 (mt)
REVERT: B  370 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.5901 (mtp180)
REVERT: B  399 LEU cc_start: 0.6103 (mt) cc_final: 0.5751 (mt)
REVERT: C  125 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6901 (mt-10)
REVERT: C  176 ARG cc_start: 0.6845 (mtt180) cc_final: 0.5766 (mtp-110)
  outliers start: 38
  outliers final: 14
  residues processed: 194
  average time/residue: 0.4847
  time to fit residues: 104.7823
Evaluate side-chains
  178 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 98 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 127 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0770
   chunk 138 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 48 optimal weight:   20.0000
   overall best weight:    0.6940

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 HIS
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5096 r_free = 0.5096 target = 0.263119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.218594 restraints weight = 29794.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.4760 rms_B_bonded: 3.49
r_work: 0.4488 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.4488
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4525 r_free = 0.4525    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4525 r_free = 0.4525    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4525
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14197  Z= 0.125
  Angle     :  0.538   8.479  19429  Z= 0.277
  Chirality :  0.041   0.251   2134
  Planarity :  0.004   0.047   2362
  Dihedral  : 14.767 178.275   2166
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.45 %
    Favored  : 80.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.59 (0.21), residues: 1603
  helix:  1.10 (0.20), residues: 706
  sheet: -0.49 (0.33), residues: 220
  loop :  0.10 (0.24), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 830 
 TYR   0.017   0.001   TYR A1125 
 PHE   0.023   0.001   PHE C 216 
 TRP   0.029   0.001   TRP A 468 
 HIS   0.010   0.001   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (14197)
  covalent geometry    : angle       0.53773 (19429)
  hydrogen bonds       : bond        0.03477 (  652)
  hydrogen bonds       : angle       4.76713 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 173
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6284 (pp)
REVERT: A  230 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.4966 (tt)
REVERT: A  340 ASP cc_start: 0.6802 (m-30) cc_final: 0.6332 (m-30)
REVERT: A  508 GLN cc_start: 0.5244 (tp40) cc_final: 0.4970 (pp30)
REVERT: A  754 ASP cc_start: 0.7574 (m-30) cc_final: 0.7259 (m-30)
REVERT: A  897 MET cc_start: 0.6548 (ttm) cc_final: 0.5803 (tmt)
REVERT: A 1035 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7424 (ppp)
REVERT: A 1094 MET cc_start: 0.6158 (OUTLIER) cc_final: 0.5693 (mmt)
REVERT: B  310 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8150 (mt)
REVERT: B  370 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5836 (mtp180)
REVERT: B  399 LEU cc_start: 0.6061 (mt) cc_final: 0.5710 (mt)
REVERT: C  125 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6928 (mt-10)
REVERT: C  176 ARG cc_start: 0.6841 (mtt180) cc_final: 0.5743 (mtp-110)
  outliers start: 36
  outliers final: 20
  residues processed: 191
  average time/residue: 0.4305
  time to fit residues: 92.1767
Evaluate side-chains
  186 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue 1035 MET
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 140 optimal weight:    5.9990
   chunk 161 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0970
   chunk 73 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 154 optimal weight:    3.9990
   chunk 128 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 148 optimal weight:    4.9990
   chunk 118 optimal weight:    9.9990
   chunk 141 optimal weight:    1.9990
   overall best weight:    1.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 253 ASN
A 291 GLN
A 370 ASN
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1180 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5062 r_free = 0.5062 target = 0.258723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.214556 restraints weight = 24167.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.4699 rms_B_bonded: 2.60
r_work: 0.4465 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.4465
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4518
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4518 r_free = 0.4518    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4518 r_free = 0.4518    target_work(ls_wunit_k1) = 0.193         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4518
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.2846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  14197  Z= 0.200
  Angle     :  0.628  11.705  19429  Z= 0.319
  Chirality :  0.043   0.165   2134
  Planarity :  0.005   0.054   2362
  Dihedral  : 14.917 178.043   2166
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 18.02 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.22 (0.21), residues: 1603
  helix:  0.80 (0.20), residues: 708
  sheet: -0.61 (0.32), residues: 224
  loop : -0.12 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 430 
 TYR   0.015   0.002   TYR A1117 
 PHE   0.022   0.002   PHE C 216 
 TRP   0.039   0.002   TRP A 468 
 HIS   0.007   0.001   HIS A 783 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (14197)
  covalent geometry    : angle       0.62828 (19429)
  hydrogen bonds       : bond        0.03986 (  652)
  hydrogen bonds       : angle       5.00930 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 162
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.6128 (pp)
REVERT: A  340 ASP cc_start: 0.6862 (m-30) cc_final: 0.6357 (m-30)
REVERT: A  425 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7026 (mmm160)
REVERT: A  508 GLN cc_start: 0.5112 (tp40) cc_final: 0.4901 (pp30)
REVERT: A  577 MET cc_start: 0.8138 (mtp) cc_final: 0.7868 (mtt)
REVERT: A  897 MET cc_start: 0.6558 (ttm) cc_final: 0.5817 (tmt)
REVERT: A 1034 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7120 (mp0)
REVERT: A 1035 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7392 (ppp)
REVERT: A 1094 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5637 (mmt)
REVERT: B  255 GLU cc_start: 0.7240 (pm20) cc_final: 0.6914 (mm-30)
REVERT: B  310 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8232 (mt)
REVERT: B  370 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.5902 (mtp180)
REVERT: B  399 LEU cc_start: 0.6070 (mt) cc_final: 0.5706 (mt)
REVERT: C  125 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6930 (mt-10)
REVERT: C  176 ARG cc_start: 0.6852 (mtt180) cc_final: 0.5752 (mtp-110)
  outliers start: 44
  outliers final: 24
  residues processed: 191
  average time/residue: 0.5004
  time to fit residues: 106.4228
Evaluate side-chains
  182 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 151
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  425 ARG
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1035 MET
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 85 optimal weight:    0.0040
   chunk 48 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 153 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1135 ASN
B 190 HIS
B 287 HIS
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5087 r_free = 0.5087 target = 0.261349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.218088 restraints weight = 28342.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.4750 rms_B_bonded: 2.92
r_work: 0.4489 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.4489
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4531 r_free = 0.4531    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4531 r_free = 0.4531    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14197  Z= 0.120
  Angle     :  0.567  11.227  19429  Z= 0.287
  Chirality :  0.040   0.152   2134
  Planarity :  0.004   0.049   2362
  Dihedral  : 14.804 178.649   2166
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.35 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.53 (0.21), residues: 1603
  helix:  1.06 (0.20), residues: 706
  sheet: -0.49 (0.32), residues: 222
  loop :  0.04 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 638 
 TYR   0.013   0.001   TYR C 265 
 PHE   0.023   0.002   PHE A1158 
 TRP   0.047   0.001   TRP A 468 
 HIS   0.011   0.001   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (14197)
  covalent geometry    : angle       0.56717 (19429)
  hydrogen bonds       : bond        0.03422 (  652)
  hydrogen bonds       : angle       4.74017 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 169
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5072 (tt)
REVERT: A  340 ASP cc_start: 0.6805 (m-30) cc_final: 0.6299 (m-30)
REVERT: A  377 TYR cc_start: 0.7127 (m-10) cc_final: 0.6834 (m-10)
REVERT: A  508 GLN cc_start: 0.5201 (tp40) cc_final: 0.4933 (pp30)
REVERT: A  577 MET cc_start: 0.8148 (mtp) cc_final: 0.7852 (mtt)
REVERT: A  754 ASP cc_start: 0.7544 (m-30) cc_final: 0.7233 (m-30)
REVERT: A  897 MET cc_start: 0.6565 (ttm) cc_final: 0.5823 (tmt)
REVERT: A 1035 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7451 (ppp)
REVERT: A 1094 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5715 (mmt)
REVERT: B  255 GLU cc_start: 0.7122 (pm20) cc_final: 0.6852 (mm-30)
REVERT: B  310 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8172 (mt)
REVERT: B  370 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.5819 (mtp180)
REVERT: C  176 ARG cc_start: 0.6848 (mtt180) cc_final: 0.5771 (mtp-110)
  outliers start: 34
  outliers final: 20
  residues processed: 188
  average time/residue: 0.5083
  time to fit residues: 106.2958
Evaluate side-chains
  186 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue 1035 MET
Chi-restraints excluded: chain A residue 1094 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  103 ASP
Chi-restraints excluded: chain B residue  104 SER
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 86 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 111 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 161 optimal weight:    2.9990
   chunk 102 optimal weight:    0.7980
   chunk 134 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 370 ASN
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1200 GLN
B 383 ASN
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.260262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.216866 restraints weight = 22486.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.4735 rms_B_bonded: 2.37
r_work: 0.4526 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4566 r_free = 0.4566    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4566 r_free = 0.4566    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14197  Z= 0.134
  Angle     :  0.586  11.486  19429  Z= 0.293
  Chirality :  0.041   0.193   2134
  Planarity :  0.004   0.049   2362
  Dihedral  : 14.799 178.494   2166
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.92 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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 (0.21), residues: 1603
  helix:  1.06 (0.20), residues: 708
  sheet: -0.50 (0.32), residues: 222
  loop :  0.04 (0.24), residues: 673

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 370 
 TYR   0.021   0.002   TYR A 461 
 PHE   0.024   0.002   PHE A1158 
 TRP   0.054   0.001   TRP A 468 
 HIS   0.013   0.001   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (14197)
  covalent geometry    : angle       0.58582 (19429)
  hydrogen bonds       : bond        0.03488 (  652)
  hydrogen bonds       : angle       4.74663 ( 1795)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 164
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.5044 (tt)
REVERT: A  340 ASP cc_start: 0.6753 (m-30) cc_final: 0.6255 (m-30)
REVERT: A  577 MET cc_start: 0.8115 (mtp) cc_final: 0.7775 (mtt)
REVERT: A  754 ASP cc_start: 0.7510 (m-30) cc_final: 0.7154 (m-30)
REVERT: A  801 ARG cc_start: 0.6377 (mmt180) cc_final: 0.6093 (mmm160)
REVERT: A  897 MET cc_start: 0.6587 (ttm) cc_final: 0.5865 (tmt)
REVERT: A 1035 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7420 (ppp)
REVERT: B  255 GLU cc_start: 0.7092 (pm20) cc_final: 0.6776 (mm-30)
REVERT: B  310 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8109 (mt)
REVERT: B  370 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5694 (mtp180)
REVERT: C  370 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7211 (mtt-85)
  outliers start: 31
  outliers final: 22
  residues processed: 180
  average time/residue: 0.4734
  time to fit residues: 95.6868
Evaluate side-chains
  182 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  377 TYR
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue 1035 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 149 optimal weight:    0.6980
   chunk 120 optimal weight:    1.9990
   chunk 129 optimal weight:    0.3980
   chunk 141 optimal weight:    2.9990
   chunk 138 optimal weight:    0.9990
   chunk 118 optimal weight:    8.9990
   chunk 22 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5098 r_free = 0.5098 target = 0.263181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4784 r_free = 0.4784 target = 0.218807 restraints weight = 24133.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.4733 rms_B_bonded: 2.64
r_work: 0.4516 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.4516
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4567 r_free = 0.4567    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4567 r_free = 0.4567    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7032
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14197  Z= 0.131
  Angle     :  0.593  11.569  19429  Z= 0.296
  Chirality :  0.042   0.410   2134
  Planarity :  0.004   0.050   2362
  Dihedral  : 14.802 178.620   2166
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.06 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.55 (0.21), residues: 1603
  helix:  1.09 (0.20), residues: 708
  sheet: -0.49 (0.32), residues: 224
  loop :  0.04 (0.24), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 370 
 TYR   0.015   0.002   TYR A 637 
 PHE   0.027   0.002   PHE A1158 
 TRP   0.053   0.001   TRP A 468 
 HIS   0.015   0.001   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (14197)
  covalent geometry    : angle       0.59255 (19429)
  hydrogen bonds       : bond        0.03429 (  652)
  hydrogen bonds       : angle       4.75404 ( 1795)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3206 Ramachandran restraints generated.
    1603 Oldfield, 0 Emsley, 1603 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.6025 (pp)
REVERT: A  230 LEU cc_start: 0.5391 (OUTLIER) cc_final: 0.4982 (tt)
REVERT: A  340 ASP cc_start: 0.6741 (m-30) cc_final: 0.6235 (m-30)
REVERT: A  577 MET cc_start: 0.8096 (mtp) cc_final: 0.7753 (mtt)
REVERT: A  754 ASP cc_start: 0.7501 (m-30) cc_final: 0.7158 (m-30)
REVERT: A  897 MET cc_start: 0.6579 (ttm) cc_final: 0.5849 (tmt)
REVERT: A 1035 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7464 (ppp)
REVERT: A 1121 GLU cc_start: 0.6100 (pm20) cc_final: 0.5469 (pm20)
REVERT: B  255 GLU cc_start: 0.7139 (pm20) cc_final: 0.6750 (mm-30)
REVERT: B  310 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8130 (mt)
REVERT: B  370 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5724 (mtp180)
REVERT: C  440 MET cc_start: 0.7351 (ttt) cc_final: 0.7134 (ttt)
  outliers start: 34
  outliers final: 23
  residues processed: 176
  average time/residue: 0.4860
  time to fit residues: 95.7796
Evaluate side-chains
  184 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 156
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  217 SER
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  377 TYR
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  627 THR
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  827 THR
Chi-restraints excluded: chain A residue  863 VAL
Chi-restraints excluded: chain A residue  869 VAL
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue 1035 MET
Chi-restraints excluded: chain A residue 1144 TYR
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  370 ARG
Chi-restraints excluded: chain C residue  138 LYS
Chi-restraints excluded: chain C residue  152 SER
Chi-restraints excluded: chain C residue  251 ASP
Chi-restraints excluded: chain C residue  345 VAL
Chi-restraints excluded: chain C residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 163 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 164 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 75 optimal weight:    0.0970
   chunk 88 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.5582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 232 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5070 r_free = 0.5070 target = 0.259853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4754 r_free = 0.4754 target = 0.217177 restraints weight = 29727.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.4721 rms_B_bonded: 3.62
r_work: 0.4438 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.4438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4485 r_free = 0.4485    target_work(ls_wunit_k1) = 0.190         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4485 r_free = 0.4485    target_work(ls_wunit_k1) = 0.190         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  14197  Z= 0.181
  Angle     :  0.636  12.748  19429  Z= 0.318
  Chirality :  0.044   0.458   2134
  Planarity :  0.005   0.048   2362
  Dihedral  : 14.890 178.424   2166
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.99 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    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:  0.30 (0.21), residues: 1603
  helix:  0.92 (0.20), residues: 705
  sheet: -0.72 (0.31), residues: 237
  loop : -0.06 (0.24), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A1124 
 TYR   0.021   0.002   TYR A 461 
 PHE   0.032   0.002   PHE A1158 
 TRP   0.054   0.002   TRP A 468 
 HIS   0.015   0.001   HIS B 287 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (14197)
  covalent geometry    : angle       0.63621 (19429)
  hydrogen bonds       : bond        0.03761 (  652)
  hydrogen bonds       : angle       4.93528 ( 1795)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4661.97 seconds
wall clock time: 80 minutes 14.40 seconds (4814.40 seconds total)