Starting phenix.real_space_refine
on Sun May 11 06:46:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avx_15686/05_2025/8avx_15686.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avx_15686/05_2025/8avx_15686.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8avx_15686/05_2025/8avx_15686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avx_15686/05_2025/8avx_15686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avx_15686/05_2025/8avx_15686.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avx_15686/05_2025/8avx_15686.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4715      2.51       5
     N    1327      2.21       5
     O    1363      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7427
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 480, 3668
          Classifications: {'peptide': 480}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 443}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 3673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 481, 3673
          Classifications: {'peptide': 481}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 444}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'BLA': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'BLA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 7.49, per 1000 atoms: 1.01
  Number of scatterers: 7427
  At special positions: 0
  Unit cell: (81.8615, 95.6487, 121.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O    1363      8.00
     N    1327      7.00
     C    4715      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: 1.93
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      41.6% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 73 through 78
    Processing helix  chain 'A' and resid 81 through 89
      removed outlier: 4.440A  pdb=" N   ALA A  87 " --> pdb=" O   PRO A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 3.524A  pdb=" N   PHE A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 168
    Processing helix  chain 'A' and resid 209 through 219
      removed outlier: 3.578A  pdb=" N   LEU A 215 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 3.749A  pdb=" N   MET A 267 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 342
      removed outlier: 3.644A  pdb=" N   ARG A 302 " --> pdb=" O   PRO A 298 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   THR A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLN A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   VAL A 318 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA A 321 " --> pdb=" O   GLN A 317 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL A 324 " --> pdb=" O   GLU A 320 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA A 325 " --> pdb=" O   ALA A 321 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE A 327 " --> pdb=" O   ASP A 323 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN A 329 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   GLU A 333 " --> pdb=" O   GLN A 329 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   HIS A 334 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   ARG A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   VAL A 338 " --> pdb=" O   HIS A 334 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA A 341 " --> pdb=" O   ARG A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 352
      removed outlier: 3.766A  pdb=" N   THR A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 352 " --> pdb=" O   PRO A 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 347 through 352'
    Processing helix  chain 'A' and resid 358 through 364
      removed outlier: 4.164A  pdb=" N   LEU A 362 " --> pdb=" O   ASP A 358 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   MET A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 398
      removed outlier: 3.511A  pdb=" N   ALA A 390 " --> pdb=" O   PRO A 386 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   THR A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.950A  pdb=" N   LEU A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 474
      removed outlier: 3.901A  pdb=" N   THR A 471 " --> pdb=" O   HIS A 467 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR A 472 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 492
      removed outlier: 3.625A  pdb=" N   GLU A 490 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 499
    Processing helix  chain 'A' and resid 503 through 521
      removed outlier: 3.738A  pdb=" N   SER A 507 " --> pdb=" O   GLY A 503 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   VAL A 508 " --> pdb=" O   GLU A 504 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE A 509 " --> pdb=" O   ARG A 505 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 81 through 89
      removed outlier: 4.418A  pdb=" N   ALA B  87 " --> pdb=" O   PRO B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 149
      removed outlier: 3.522A  pdb=" N   PHE B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 168
    Processing helix  chain 'B' and resid 209 through 219
      removed outlier: 3.581A  pdb=" N   LEU B 215 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ARG B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 268
      removed outlier: 3.751A  pdb=" N   MET B 267 " --> pdb=" O   TYR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 342
      removed outlier: 3.675A  pdb=" N   ARG B 302 " --> pdb=" O   PRO B 298 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   THR B 303 " --> pdb=" O   PRO B 299 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   THR B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   GLN B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL B 318 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA B 321 " --> pdb=" O   GLN B 317 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL B 324 " --> pdb=" O   GLU B 320 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA B 325 " --> pdb=" O   ALA B 321 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   PHE B 327 " --> pdb=" O   ASP B 323 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLN B 329 " --> pdb=" O   ALA B 325 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   SER B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   GLU B 333 " --> pdb=" O   GLN B 329 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   HIS B 334 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL B 338 " --> pdb=" O   HIS B 334 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ALA B 341 " --> pdb=" O   ARG B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 352
      removed outlier: 3.766A  pdb=" N   THR B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU B 352 " --> pdb=" O   PRO B 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 347 through 352'
    Processing helix  chain 'B' and resid 358 through 364
      removed outlier: 4.171A  pdb=" N   LEU B 362 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 398
      removed outlier: 3.512A  pdb=" N   ALA B 390 " --> pdb=" O   PRO B 386 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B 393 " --> pdb=" O   ASP B 389 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLU B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR B 397 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 412
      removed outlier: 3.948A  pdb=" N   LEU B 411 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 474
      removed outlier: 3.894A  pdb=" N   THR B 471 " --> pdb=" O   HIS B 467 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR B 472 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 492
      removed outlier: 3.624A  pdb=" N   GLU B 490 " --> pdb=" O   GLY B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 499
    Processing helix  chain 'B' and resid 503 through 521
      removed outlier: 3.716A  pdb=" N   SER B 507 " --> pdb=" O   GLY B 503 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL B 508 " --> pdb=" O   GLU B 504 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE B 509 " --> pdb=" O   ARG B 505 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B 510 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.774A  pdb=" N   VAL A  51 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASP A  45 " --> pdb=" O   VAL A  51 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   SER A  55 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   LEU A  41 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A 103 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203
      removed outlier: 3.689A  pdb=" N   THR A 183 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   LEU A 175 " --> pdb=" O   ILE A 187 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL A 173 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA A 288 " --> pdb=" O   MET A 174 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   TRP A 284 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   VAL A 277 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   LEU A 286 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   VAL A 275 " --> pdb=" O   LEU A 286 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   ALA A 288 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   LEU A 273 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 380
      removed outlier: 4.585A  pdb=" N   GLU A 436 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 424 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 446
    Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35
      removed outlier: 6.775A  pdb=" N   VAL B  51 " --> pdb=" O   ASP B  45 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASP B  45 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER B  55 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU B  41 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 103 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203
      removed outlier: 3.689A  pdb=" N   THR B 183 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LEU B 175 " --> pdb=" O   ILE B 187 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   GLU B 189 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL B 173 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA B 288 " --> pdb=" O   MET B 174 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   TRP B 284 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL B 277 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL B 275 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   ALA B 288 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   LEU B 273 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 375 through 380
      removed outlier: 4.568A  pdb=" N   GLU B 436 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLY B 424 " --> pdb=" O   ARG B 442 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    906 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 2.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1481
        1.33 -     1.45: 1744
        1.45 -     1.57: 4349
        1.57 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 7610
  Sorted by residual:
  bond pdb=" C2B BLA B1000 "
       pdb=" C3B BLA B1000 "
    ideal  model  delta    sigma   weight residual
    1.357  1.432 -0.075 2.00e-02 2.50e+03 1.39e+01
  bond pdb=" C2B BLA A1000 "
       pdb=" C3B BLA A1000 "
    ideal  model  delta    sigma   weight residual
    1.357  1.429 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C1D BLA A1000 "
       pdb=" CHD BLA A1000 "
    ideal  model  delta    sigma   weight residual
    1.440  1.373  0.067 2.00e-02 2.50e+03 1.12e+01
  bond pdb=" C2C BLA A1000 "
       pdb=" C3C BLA A1000 "
    ideal  model  delta    sigma   weight residual
    1.351  1.415 -0.064 2.00e-02 2.50e+03 1.03e+01
  bond pdb=" C1D BLA B1000 "
       pdb=" CHD BLA B1000 "
    ideal  model  delta    sigma   weight residual
    1.440  1.377  0.063 2.00e-02 2.50e+03 1.00e+01
  ... (remaining 7605 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 8600
        1.83 -     3.65: 1643
        3.65 -     5.48: 156
        5.48 -     7.30: 8
        7.30 -     9.13: 3
  Bond angle restraints: 10410
  Sorted by residual:
  angle pdb=" C   PHE B 203 "
        pdb=" CA  PHE B 203 "
        pdb=" CB  PHE B 203 "
      ideal   model   delta    sigma   weight residual
     108.87  115.23   -6.36 1.55e+00 4.16e-01 1.68e+01
  angle pdb=" C   PHE A 203 "
        pdb=" CA  PHE A 203 "
        pdb=" CB  PHE A 203 "
      ideal   model   delta    sigma   weight residual
     108.87  115.05   -6.18 1.55e+00 4.16e-01 1.59e+01
  angle pdb=" CB  ARG A 375 "
        pdb=" CG  ARG A 375 "
        pdb=" CD  ARG A 375 "
      ideal   model   delta    sigma   weight residual
     111.30  120.43   -9.13 2.30e+00 1.89e-01 1.58e+01
  angle pdb=" C   PRO B 384 "
        pdb=" N   ALA B 385 "
        pdb=" CA  ALA B 385 "
      ideal   model   delta    sigma   weight residual
     120.09  124.82   -4.73 1.25e+00 6.40e-01 1.43e+01
  angle pdb=" C   PRO A 384 "
        pdb=" N   ALA A 385 "
        pdb=" CA  ALA A 385 "
      ideal   model   delta    sigma   weight residual
     120.09  124.79   -4.70 1.25e+00 6.40e-01 1.41e+01
  ... (remaining 10405 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3915
       17.27 -    34.54: 440
       34.54 -    51.80: 120
       51.80 -    69.07: 71
       69.07 -    86.34: 6
  Dihedral angle restraints: 4552
    sinusoidal: 1808
      harmonic: 2744
  Sorted by residual:
  dihedral pdb=" CA  HIS B 219 "
           pdb=" C   HIS B 219 "
           pdb=" N   LEU B 220 "
           pdb=" CA  LEU B 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.72  -19.28     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" CA  HIS A 219 "
           pdb=" C   HIS A 219 "
           pdb=" N   LEU A 220 "
           pdb=" CA  LEU A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.76  -19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CG  ARG B 514 "
           pdb=" CD  ARG B 514 "
           pdb=" NE  ARG B 514 "
           pdb=" CZ  ARG B 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.38   44.62     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 4549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 627
       0.050 -    0.100: 285
       0.100 -    0.151: 190
       0.151 -    0.201: 54
       0.201 -    0.251: 17
  Chirality restraints: 1173
  Sorted by residual:
  chirality pdb=" CB  VAL A 237 "
            pdb=" CA  VAL A 237 "
            pdb=" CG1 VAL A 237 "
            pdb=" CG2 VAL A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CB  VAL A 449 "
            pdb=" CA  VAL A 449 "
            pdb=" CG1 VAL A 449 "
            pdb=" CG2 VAL A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ASN B 243 "
            pdb=" N   ASN B 243 "
            pdb=" C   ASN B 243 "
            pdb=" CB  ASN B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 1170 not shown)

  Planarity restraints: 1364
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA B1000 "   -0.001 2.00e-02 2.50e+03   2.84e-01 2.01e+03
        pdb=" C1D BLA B1000 "    0.520 2.00e-02 2.50e+03
        pdb=" C2C BLA B1000 "   -0.007 2.00e-02 2.50e+03
        pdb=" C3C BLA B1000 "   -0.040 2.00e-02 2.50e+03
        pdb=" C4C BLA B1000 "   -0.264 2.00e-02 2.50e+03
        pdb=" CAC BLA B1000 "    0.147 2.00e-02 2.50e+03
        pdb=" CHD BLA B1000 "   -0.254 2.00e-02 2.50e+03
        pdb=" CMC BLA B1000 "    0.055 2.00e-02 2.50e+03
        pdb=" NC  BLA B1000 "   -0.503 2.00e-02 2.50e+03
        pdb=" OC  BLA B1000 "    0.347 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  BLA B1000 "   -0.384 2.00e-02 2.50e+03   2.82e-01 1.98e+03
        pdb=" OB  BLA B1000 "    0.184 2.00e-02 2.50e+03
        pdb=" C1B BLA B1000 "   -0.180 2.00e-02 2.50e+03
        pdb=" C2B BLA B1000 "   -0.174 2.00e-02 2.50e+03
        pdb=" C3B BLA B1000 "    0.071 2.00e-02 2.50e+03
        pdb=" C4A BLA B1000 "    0.543 2.00e-02 2.50e+03
        pdb=" C4B BLA B1000 "   -0.019 2.00e-02 2.50e+03
        pdb=" CAB BLA B1000 "    0.348 2.00e-02 2.50e+03
        pdb=" CHB BLA B1000 "   -0.032 2.00e-02 2.50e+03
        pdb=" CMB BLA B1000 "   -0.357 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C BLA A1000 "   -0.034 2.00e-02 2.50e+03   2.78e-01 1.93e+03
        pdb=" C1D BLA A1000 "    0.551 2.00e-02 2.50e+03
        pdb=" C2C BLA A1000 "    0.033 2.00e-02 2.50e+03
        pdb=" C3C BLA A1000 "   -0.075 2.00e-02 2.50e+03
        pdb=" C4C BLA A1000 "   -0.247 2.00e-02 2.50e+03
        pdb=" CAC BLA A1000 "    0.008 2.00e-02 2.50e+03
        pdb=" CHD BLA A1000 "   -0.175 2.00e-02 2.50e+03
        pdb=" CMC BLA A1000 "    0.210 2.00e-02 2.50e+03
        pdb=" NC  BLA A1000 "   -0.515 2.00e-02 2.50e+03
        pdb=" OC  BLA A1000 "    0.243 2.00e-02 2.50e+03
  ... (remaining 1361 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1574
        2.83 -     3.35: 6100
        3.35 -     3.87: 11931
        3.87 -     4.38: 13281
        4.38 -     4.90: 23340
  Nonbonded interactions: 56226
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 107 "
            pdb=" N   GLY A 109 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" O   LEU B 516 "
            pdb=" OG  SER B 519 "
     model   vdw
     2.584 3.040
  nonbonded pdb=" O   LEU A 516 "
            pdb=" OG  SER A 519 "
     model   vdw
     2.585 3.040
  nonbonded pdb=" O   GLY A  39 "
            pdb=" ND2 ASN A  57 "
     model   vdw
     2.600 3.120
  nonbonded pdb=" O   GLY B  39 "
            pdb=" ND2 ASN B  57 "
     model   vdw
     2.601 3.120
  ... (remaining 56221 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 22 through 107 or resid 109 through 521 or resid 1000))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.040
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.075   7610  Z= 0.512
  Angle     :  1.384   9.131  10410  Z= 0.921
  Chirality :  0.079   0.251   1173
  Planarity :  0.015   0.284   1364
  Dihedral  : 17.707  86.341   2778
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.54 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 11.64 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.22), residues: 947
  helix: -3.67 (0.16), residues: 369
  sheet: -1.34 (0.36), residues: 180
  loop : -2.13 (0.26), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 451 
 HIS   0.006   0.002   HIS A 349 
 PHE   0.011   0.002   PHE B 170 
 TYR   0.030   0.003   TYR B 307 
 ARG   0.014   0.001   ARG A 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27770 (  322)
  hydrogen bonds       : angle       9.75593 (  906)
  covalent geometry    : bond        0.00785 ( 7610)
  covalent geometry    : angle       1.38375 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.921 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6840 (mtp180) cc_final: 0.5248 (tpt170)
REVERT: A  466 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.1647 (mmp80)
REVERT: B  227 THR cc_start: 0.7630 (p) cc_final: 0.7188 (p)
REVERT: B  381 GLU cc_start: 0.7836 (pm20) cc_final: 0.7243 (pp20)
REVERT: B  493 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7326 (t0)
  outliers start: 32
  outliers final: 4
  residues processed: 174
  average time/residue: 0.2407
  time to fit residues: 53.7874
Evaluate side-chains
  94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  493 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 49 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0370
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN
A 110 HIS
A 239 ASN
** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 513 ASN
B 290 HIS
B 334 HIS
B 335 HIS
B 410 GLN
B 513 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.190739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.165491 restraints weight = 13076.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.169486 restraints weight = 7453.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.172161 restraints weight = 5049.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6341
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7610  Z= 0.140
  Angle     :  0.656   8.232  10410  Z= 0.309
  Chirality :  0.041   0.132   1173
  Planarity :  0.004   0.031   1364
  Dihedral  :  7.338  80.891   1103
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.87 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.25), residues: 947
  helix: -2.05 (0.23), residues: 372
  sheet: -0.83 (0.36), residues: 193
  loop : -1.44 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 434 
 HIS   0.008   0.002   HIS B 335 
 PHE   0.018   0.002   PHE B 126 
 TYR   0.018   0.002   TYR A 479 
 ARG   0.004   0.000   ARG B 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  322)
  hydrogen bonds       : angle       5.64866 (  906)
  covalent geometry    : bond        0.00315 ( 7610)
  covalent geometry    : angle       0.65603 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 99
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6841 (mtp180) cc_final: 0.5682 (tpt170)
REVERT: A  363 MET cc_start: 0.5505 (tpp) cc_final: 0.5171 (tpp)
REVERT: A  466 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.1677 (mmt180)
REVERT: B   45 ASP cc_start: 0.5287 (t70) cc_final: 0.5004 (m-30)
REVERT: B  313 SER cc_start: 0.7856 (m) cc_final: 0.7623 (p)
REVERT: B  493 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7287 (t0)
  outliers start: 38
  outliers final: 10
  residues processed: 131
  average time/residue: 0.2109
  time to fit residues: 36.5569
Evaluate side-chains
  92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  493 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0060
   chunk 83 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
B  57 ASN
B 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.187713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.162591 restraints weight = 13661.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.166336 restraints weight = 7971.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.168882 restraints weight = 5516.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.4261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7610  Z= 0.132
  Angle     :  0.633   8.970  10410  Z= 0.297
  Chirality :  0.042   0.141   1173
  Planarity :  0.005   0.038   1364
  Dihedral  :  6.925  77.585   1098
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.97 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.25), residues: 947
  helix: -1.33 (0.25), residues: 366
  sheet: -0.58 (0.36), residues: 190
  loop : -1.21 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 284 
 HIS   0.005   0.001   HIS B 467 
 PHE   0.018   0.002   PHE B 327 
 TYR   0.014   0.002   TYR B 295 
 ARG   0.005   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03665 (  322)
  hydrogen bonds       : angle       5.21844 (  906)
  covalent geometry    : bond        0.00307 ( 7610)
  covalent geometry    : angle       0.63304 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6768 (mtp180) cc_final: 0.5615 (tpt170)
REVERT: A  466 ARG cc_start: 0.4953 (OUTLIER) cc_final: 0.1609 (mmt180)
REVERT: B   45 ASP cc_start: 0.5441 (t70) cc_final: 0.4989 (m-30)
REVERT: B  125 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.5835 (mm-30)
REVERT: B  355 PRO cc_start: 0.6732 (Cg_exo) cc_final: 0.6441 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6302 (tp30) cc_final: 0.5695 (pt0)
REVERT: B  493 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7266 (t0)
  outliers start: 27
  outliers final: 14
  residues processed: 101
  average time/residue: 0.2000
  time to fit residues: 27.6248
Evaluate side-chains
  78 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  125 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  493 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 17 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 329 GLN
B 513 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.185730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.160788 restraints weight = 13663.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.164486 restraints weight = 8089.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.166872 restraints weight = 5628.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.4246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6479
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7610  Z= 0.130
  Angle     :  0.622   9.659  10410  Z= 0.287
  Chirality :  0.042   0.162   1173
  Planarity :  0.005   0.039   1364
  Dihedral  :  6.675  76.315   1098
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.90 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.26), residues: 947
  helix: -0.91 (0.26), residues: 372
  sheet: -0.58 (0.36), residues: 189
  loop : -1.02 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 376 
 HIS   0.007   0.001   HIS A 484 
 PHE   0.019   0.002   PHE B 327 
 TYR   0.017   0.002   TYR A 479 
 ARG   0.003   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  322)
  hydrogen bonds       : angle       4.91455 (  906)
  covalent geometry    : bond        0.00301 ( 7610)
  covalent geometry    : angle       0.62191 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6767 (mtp180) cc_final: 0.5717 (tpt170)
REVERT: A  308 LEU cc_start: 0.8168 (mt) cc_final: 0.7966 (mp)
REVERT: A  363 MET cc_start: 0.6090 (tpp) cc_final: 0.5828 (tpp)
REVERT: A  466 ARG cc_start: 0.5160 (OUTLIER) cc_final: 0.1729 (mmt180)
REVERT: B   45 ASP cc_start: 0.5339 (t70) cc_final: 0.4924 (m-30)
REVERT: B  355 PRO cc_start: 0.6537 (Cg_exo) cc_final: 0.6279 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6602 (tp30) cc_final: 0.6134 (pt0)
REVERT: B  493 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7338 (t0)
  outliers start: 25
  outliers final: 15
  residues processed: 96
  average time/residue: 0.2132
  time to fit residues: 27.5460
Evaluate side-chains
  82 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  493 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0570
   chunk 83 optimal weight:    0.0070
   chunk 6 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 57 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.2516

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

Flipped N/Q/H residues before XYZ refinement:
A 484 HIS
B 398 GLN
B 513 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.189783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.165523 restraints weight = 13112.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.169124 restraints weight = 7825.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.171450 restraints weight = 5446.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7610  Z= 0.091
  Angle     :  0.571   9.550  10410  Z= 0.260
  Chirality :  0.040   0.146   1173
  Planarity :  0.004   0.040   1364
  Dihedral  :  6.150  87.059   1098
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 21.83 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.27), residues: 947
  helix: -0.52 (0.27), residues: 374
  sheet: -0.45 (0.36), residues: 188
  loop : -0.67 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 284 
 HIS   0.011   0.001   HIS A 484 
 PHE   0.020   0.001   PHE B 327 
 TYR   0.019   0.002   TYR A 263 
 ARG   0.004   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02739 (  322)
  hydrogen bonds       : angle       4.54885 (  906)
  covalent geometry    : bond        0.00209 ( 7610)
  covalent geometry    : angle       0.57058 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6690 (mtp180) cc_final: 0.5675 (tpt170)
REVERT: A  199 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7542 (tt)
REVERT: A  466 ARG cc_start: 0.5077 (OUTLIER) cc_final: 0.1628 (mmt180)
REVERT: B   45 ASP cc_start: 0.5199 (t70) cc_final: 0.4575 (m-30)
REVERT: B  355 PRO cc_start: 0.6384 (Cg_exo) cc_final: 0.6142 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6443 (tp30) cc_final: 0.5933 (pt0)
  outliers start: 21
  outliers final: 11
  residues processed: 94
  average time/residue: 0.2003
  time to fit residues: 25.4527
Evaluate side-chains
  81 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  238 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0000
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
B  57 ASN
B 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.185051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.160846 restraints weight = 13543.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.164259 restraints weight = 8272.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.166492 restraints weight = 5864.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6503
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7610  Z= 0.126
  Angle     :  0.613   9.165  10410  Z= 0.285
  Chirality :  0.042   0.173   1173
  Planarity :  0.005   0.040   1364
  Dihedral  :  6.339  84.428   1096
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 21.03 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.27), residues: 947
  helix: -0.45 (0.27), residues: 377
  sheet: -0.51 (0.36), residues: 190
  loop : -0.73 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 284 
 HIS   0.013   0.001   HIS A 484 
 PHE   0.031   0.002   PHE A 327 
 TYR   0.013   0.002   TYR A 263 
 ARG   0.011   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  322)
  hydrogen bonds       : angle       4.69451 (  906)
  covalent geometry    : bond        0.00296 ( 7610)
  covalent geometry    : angle       0.61275 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.775 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6844 (mtp180) cc_final: 0.5881 (tpt170)
REVERT: A  199 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7550 (tt)
REVERT: A  202 ARG cc_start: 0.6453 (mmp80) cc_final: 0.6141 (mmp80)
REVERT: B   45 ASP cc_start: 0.4971 (t70) cc_final: 0.4674 (m-30)
REVERT: B  355 PRO cc_start: 0.6222 (Cg_exo) cc_final: 0.5989 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6633 (tp30) cc_final: 0.6315 (pt0)
  outliers start: 27
  outliers final: 23
  residues processed: 90
  average time/residue: 0.2052
  time to fit residues: 24.9509
Evaluate side-chains
  88 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 64
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  138 HIS
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  376 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0870
   chunk 46 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0170
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 92 optimal weight:    0.2980
   overall best weight:    0.2174

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
B 398 GLN
B 513 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.188571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.164687 restraints weight = 13432.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.168228 restraints weight = 8043.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.170594 restraints weight = 5613.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7610  Z= 0.091
  Angle     :  0.569   9.132  10410  Z= 0.260
  Chirality :  0.040   0.211   1173
  Planarity :  0.004   0.040   1364
  Dihedral  :  6.038  89.040   1096
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 22.22 %
    Favored  : 75.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.27), residues: 947
  helix: -0.03 (0.28), residues: 370
  sheet: -0.39 (0.36), residues: 190
  loop : -0.58 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 467 
 PHE   0.019   0.001   PHE B 327 
 TYR   0.022   0.002   TYR A 307 
 ARG   0.007   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02844 (  322)
  hydrogen bonds       : angle       4.46074 (  906)
  covalent geometry    : bond        0.00211 ( 7610)
  covalent geometry    : angle       0.56934 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.822 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6779 (mtp180) cc_final: 0.5838 (tpt170)
REVERT: A  199 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7511 (tt)
REVERT: A  306 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7220 (mp0)
REVERT: A  376 TRP cc_start: 0.6174 (p-90) cc_final: 0.5409 (p-90)
REVERT: B  432 GLU cc_start: 0.6371 (tp30) cc_final: 0.6083 (pt0)
  outliers start: 18
  outliers final: 12
  residues processed: 89
  average time/residue: 0.2239
  time to fit residues: 26.3674
Evaluate side-chains
  80 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  376 TRP
Chi-restraints excluded: chain B residue  513 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.182232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.159134 restraints weight = 13343.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.161124 restraints weight = 8680.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.162566 restraints weight = 6110.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.5337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7610  Z= 0.144
  Angle     :  0.644   8.803  10410  Z= 0.300
  Chirality :  0.043   0.202   1173
  Planarity :  0.005   0.039   1364
  Dihedral  :  6.089  62.855   1096
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 21.83 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.27), residues: 947
  helix: -0.25 (0.27), residues: 380
  sheet: -0.56 (0.36), residues: 195
  loop : -0.59 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 284 
 HIS   0.011   0.002   HIS A 484 
 PHE   0.018   0.002   PHE B 327 
 TYR   0.018   0.002   TYR A 307 
 ARG   0.005   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03562 (  322)
  hydrogen bonds       : angle       4.76767 (  906)
  covalent geometry    : bond        0.00342 ( 7610)
  covalent geometry    : angle       0.64447 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6991 (mtp180) cc_final: 0.5875 (tpt170)
REVERT: A  306 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7149 (mp0)
REVERT: A  376 TRP cc_start: 0.6156 (p-90) cc_final: 0.5412 (p-90)
REVERT: B  355 PRO cc_start: 0.6185 (Cg_exo) cc_final: 0.5963 (Cg_endo)
  outliers start: 25
  outliers final: 22
  residues processed: 90
  average time/residue: 0.2019
  time to fit residues: 24.5513
Evaluate side-chains
  88 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  138 HIS
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  261 MET
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  376 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0980
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    0.2980
   chunk 57 optimal weight:    0.4980
   chunk 28 optimal weight:    0.4980
   chunk 12 optimal weight:    0.5980
   chunk 92 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.186216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.162034 restraints weight = 13494.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.165343 restraints weight = 8181.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.167675 restraints weight = 5738.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6467
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   7610  Z= 0.105
  Angle     :  0.600   9.110  10410  Z= 0.277
  Chirality :  0.041   0.211   1173
  Planarity :  0.005   0.040   1364
  Dihedral  :  5.619  56.426   1096
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.49 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.28), residues: 947
  helix:  0.09 (0.28), residues: 370
  sheet: -0.48 (0.36), residues: 194
  loop : -0.47 (0.33), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 284 
 HIS   0.006   0.001   HIS A 484 
 PHE   0.016   0.001   PHE B 327 
 TYR   0.015   0.002   TYR B 307 
 ARG   0.004   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02978 (  322)
  hydrogen bonds       : angle       4.49100 (  906)
  covalent geometry    : bond        0.00247 ( 7610)
  covalent geometry    : angle       0.60009 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6911 (mtp180) cc_final: 0.5977 (tpt170)
REVERT: A  199 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7455 (tt)
REVERT: A  306 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7167 (mp0)
REVERT: A  376 TRP cc_start: 0.5929 (p-90) cc_final: 0.5259 (p-90)
  outliers start: 23
  outliers final: 20
  residues processed: 86
  average time/residue: 0.2006
  time to fit residues: 23.3942
Evaluate side-chains
  85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  144 MET
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  376 TRP
Chi-restraints excluded: chain B residue  513 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 38 optimal weight:    8.9990
   chunk 86 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0570
   overall best weight:    1.5302

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

Flipped N/Q/H residues before XYZ refinement:
B 513 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.178193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.155552 restraints weight = 13632.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.157326 restraints weight = 8633.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.158224 restraints weight = 6511.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.5772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   7610  Z= 0.219
  Angle     :  0.774  10.070  10410  Z= 0.365
  Chirality :  0.047   0.215   1173
  Planarity :  0.006   0.038   1364
  Dihedral  :  6.493  57.543   1096
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.88 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.09 (0.27), residues: 947
  helix: -0.49 (0.27), residues: 381
  sheet: -0.43 (0.37), residues: 192
  loop : -0.93 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP B 284 
 HIS   0.010   0.002   HIS A 484 
 PHE   0.020   0.003   PHE B 327 
 TYR   0.018   0.002   TYR B 295 
 ARG   0.009   0.001   ARG B 514 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04549 (  322)
  hydrogen bonds       : angle       5.26615 (  906)
  covalent geometry    : bond        0.00517 ( 7610)
  covalent geometry    : angle       0.77431 (10410)

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6971 (mtp180) cc_final: 0.5978 (tpt170)
REVERT: A  138 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6190 (t-90)
REVERT: A  376 TRP cc_start: 0.5953 (p-90) cc_final: 0.5223 (p-90)
REVERT: B  355 PRO cc_start: 0.6313 (Cg_exo) cc_final: 0.6092 (Cg_endo)
  outliers start: 23
  outliers final: 17
  residues processed: 83
  average time/residue: 0.2099
  time to fit residues: 23.4555
Evaluate side-chains
  78 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  138 HIS
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 91 optimal weight:    0.1980
   chunk 68 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 266 ASN
B 513 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.182670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.159881 restraints weight = 13353.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.162767 restraints weight = 8320.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.163945 restraints weight = 5710.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.5865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7610  Z= 0.125
  Angle     :  0.645   9.179  10410  Z= 0.299
  Chirality :  0.042   0.209   1173
  Planarity :  0.005   0.039   1364
  Dihedral  :  5.889  58.912   1096
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.68 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.27), residues: 947
  helix: -0.06 (0.27), residues: 377
  sheet: -0.40 (0.37), residues: 192
  loop : -0.71 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 284 
 HIS   0.006   0.001   HIS A 484 
 PHE   0.015   0.002   PHE B 327 
 TYR   0.019   0.002   TYR A 307 
 ARG   0.006   0.000   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03374 (  322)
  hydrogen bonds       : angle       4.75822 (  906)
  covalent geometry    : bond        0.00296 ( 7610)
  covalent geometry    : angle       0.64451 (10410)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2716.96 seconds
wall clock time: 48 minutes 9.38 seconds (2889.38 seconds total)