Starting phenix.real_space_refine
on Wed Mar 12 09:13:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avx_15686/03_2025/8avx_15686.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avx_15686/03_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_15686/03_2025/8avx_15686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avx_15686/03_2025/8avx_15686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avx_15686/03_2025/8avx_15686.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avx_15686/03_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-5624/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: 5.89, per 1000 atoms: 0.79
  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: 1.62
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.83
  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: 2.09

  Time building geometry restraints manager: 1.94 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:             5.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.000
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  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:   29.880
-------------------------------------------------------------------------------
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= 0.516
  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 

*********************** 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  : 0.802 
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: 0.2301
  time to fit residues: 51.4266
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  : 0.763 
-------------------------------------------------------------------------------
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 = 0.165493 restraints weight = 13076.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.169538 restraints weight = 7454.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.172159 restraints weight = 5040.455|
|-----------------------------------------------------------------------------|
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= 0.212
  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 

*********************** 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  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6843 (mtp180) cc_final: 0.5682 (tpt170)
REVERT: A  363 MET cc_start: 0.5512 (tpp) cc_final: 0.5181 (tpp)
REVERT: A  466 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.1676 (mmt180)
REVERT: B   45 ASP cc_start: 0.5288 (t70) cc_final: 0.5005 (m-30)
REVERT: B  313 SER cc_start: 0.7855 (m) cc_final: 0.7622 (p)
REVERT: B  493 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7289 (t0)
  outliers start: 38
  outliers final: 10
  residues processed: 131
  average time/residue: 0.2040
  time to fit residues: 35.5489
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  : 0.734 
-------------------------------------------------------------------------------
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:    0.1980
   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:    0.0030
   chunk 83 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.4490 r_free = 0.4490 target = 0.188646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.163472 restraints weight = 13616.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.167307 restraints weight = 7930.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.169902 restraints weight = 5470.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6415
moved from start:          0.3741

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= 0.191
  Angle     :  0.617   8.912  10410  Z= 0.289
  Chirality :  0.041   0.138   1173
  Planarity :  0.005   0.038   1364
  Dihedral  :  6.869  77.319   1098
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.44 %
    Favored  : 76.85 %
  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: -1.77 (0.26), residues: 947
  helix: -1.28 (0.26), residues: 366
  sheet: -0.52 (0.36), residues: 189
  loop : -1.20 (0.29), residues: 392

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   0.012   0.002   TYR B 295 
 ARG   0.003   0.000   ARG A 172 

*********************** 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: 28
    poor density    : 76
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6763 (mtp180) cc_final: 0.5605 (tpt170)
REVERT: A  466 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.1626 (mmt180)
REVERT: B   45 ASP cc_start: 0.5408 (t70) cc_final: 0.4948 (m-30)
REVERT: B  125 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.5831 (mm-30)
REVERT: B  355 PRO cc_start: 0.6732 (Cg_exo) cc_final: 0.6451 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6272 (tp30) cc_final: 0.5561 (pt0)
REVERT: B  493 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7264 (t0)
  outliers start: 28
  outliers final: 14
  residues processed: 102
  average time/residue: 0.1886
  time to fit residues: 26.3485
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  : 0.733 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0870
   chunk 72 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4481 r_free = 0.4481 target = 0.187655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.162691 restraints weight = 13552.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.166444 restraints weight = 8010.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.168892 restraints weight = 5530.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6432
moved from start:          0.4129

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= 0.172
  Angle     :  0.605   9.771  10410  Z= 0.275
  Chirality :  0.041   0.149   1173
  Planarity :  0.004   0.039   1364
  Dihedral  :  6.651  79.061   1098
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.50 %
    Favored  : 76.32 %
  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: -1.30 (0.26), residues: 947
  helix: -0.81 (0.27), residues: 369
  sheet: -0.49 (0.36), residues: 187
  loop : -0.89 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 376 
 HIS   0.008   0.001   HIS A 484 
 PHE   0.019   0.002   PHE B 327 
 TYR   0.014   0.002   TYR A 307 
 ARG   0.003   0.000   ARG A 202 

*********************** 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
  94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6720 (mtp180) cc_final: 0.5669 (tpt170)
REVERT: A  363 MET cc_start: 0.6113 (tpp) cc_final: 0.5833 (tpp)
REVERT: A  364 ARG cc_start: 0.6782 (mtt180) cc_final: 0.6571 (mtt180)
REVERT: A  466 ARG cc_start: 0.5161 (OUTLIER) cc_final: 0.1786 (mmt180)
REVERT: B   45 ASP cc_start: 0.5299 (t70) cc_final: 0.4872 (m-30)
REVERT: B  355 PRO cc_start: 0.6621 (Cg_exo) cc_final: 0.6370 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6294 (tp30) cc_final: 0.5820 (pt0)
REVERT: B  493 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7290 (t0)
  outliers start: 24
  outliers final: 15
  residues processed: 89
  average time/residue: 0.2429
  time to fit residues: 29.7036
Evaluate side-chains
  79 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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  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   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:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0770
   chunk 83 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0770
   chunk 46 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 31 optimal weight:    0.1980
   overall best weight:    0.2696

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.190443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.166067 restraints weight = 13175.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.169657 restraints weight = 7831.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.172009 restraints weight = 5462.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6375
moved from start:          0.4382

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= 0.139
  Angle     :  0.560   9.630  10410  Z= 0.255
  Chirality :  0.040   0.151   1173
  Planarity :  0.004   0.040   1364
  Dihedral  :  6.165  78.164   1098
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 21.30 %
    Favored  : 76.06 %
  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: -0.89 (0.27), residues: 947
  helix: -0.40 (0.27), residues: 370
  sheet: -0.42 (0.36), residues: 188
  loop : -0.67 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 284 
 HIS   0.009   0.001   HIS A 484 
 PHE   0.025   0.001   PHE A 327 
 TYR   0.024   0.001   TYR A 307 
 ARG   0.003   0.000   ARG A 202 

*********************** 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
  92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6625 (mtp180) cc_final: 0.5626 (tpt170)
REVERT: A  199 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7735 (tt)
REVERT: A  466 ARG cc_start: 0.5069 (OUTLIER) cc_final: 0.1689 (mmt180)
REVERT: B   45 ASP cc_start: 0.5171 (t70) cc_final: 0.4548 (m-30)
REVERT: B  355 PRO cc_start: 0.6393 (Cg_exo) cc_final: 0.6156 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6277 (tp30) cc_final: 0.5834 (pt0)
  outliers start: 20
  outliers final: 10
  residues processed: 89
  average time/residue: 0.2007
  time to fit residues: 24.2675
Evaluate side-chains
  78 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
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  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:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 262 GLN
A 484 HIS
B 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.183460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.159624 restraints weight = 13319.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.162911 restraints weight = 8554.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.164091 restraints weight = 5524.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.4894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7610  Z= 0.239
  Angle     :  0.641   9.419  10410  Z= 0.302
  Chirality :  0.043   0.200   1173
  Planarity :  0.005   0.041   1364
  Dihedral  :  6.443  83.387   1096
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.43 %
    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: -1.11 (0.27), residues: 947
  helix: -0.55 (0.27), residues: 383
  sheet: -0.50 (0.36), residues: 190
  loop : -0.85 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 284 
 HIS   0.012   0.002   HIS A 484 
 PHE   0.023   0.002   PHE A 327 
 TYR   0.023   0.002   TYR A 307 
 ARG   0.005   0.000   ARG A 202 

*********************** 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
  95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6904 (mtp180) cc_final: 0.5807 (tpt170)
REVERT: B   45 ASP cc_start: 0.5003 (t70) cc_final: 0.4710 (m-30)
REVERT: B  355 PRO cc_start: 0.6206 (Cg_exo) cc_final: 0.5981 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6550 (tp30) cc_final: 0.6338 (pt0)
  outliers start: 24
  outliers final: 20
  residues processed: 92
  average time/residue: 0.2067
  time to fit residues: 25.8003
Evaluate side-chains
  84 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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  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  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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0010
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0970
   chunk 78 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 398 GLN
** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.185036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.161857 restraints weight = 13222.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.164816 restraints weight = 8284.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.165965 restraints weight = 5476.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6478
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7610  Z= 0.168
  Angle     :  0.584   9.233  10410  Z= 0.271
  Chirality :  0.041   0.195   1173
  Planarity :  0.005   0.042   1364
  Dihedral  :  6.270  88.894   1096
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.22 %
    Favored  : 74.74 %
  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: -0.74 (0.27), residues: 947
  helix: -0.23 (0.28), residues: 374
  sheet: -0.40 (0.37), residues: 190
  loop : -0.60 (0.32), residues: 383

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   0.023   0.002   TYR A 307 
 ARG   0.009   0.000   ARG A 202 

*********************** 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: 23
    poor density    : 70
  time to evaluate  : 0.734 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6895 (mtp180) cc_final: 0.5783 (tpt170)
REVERT: A  199 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7464 (tt)
REVERT: A  306 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7272 (mp0)
REVERT: A  350 ASP cc_start: 0.6584 (p0) cc_final: 0.5789 (t70)
REVERT: A  376 TRP cc_start: 0.6188 (p-90) cc_final: 0.5362 (p-90)
REVERT: B  355 PRO cc_start: 0.6252 (Cg_exo) cc_final: 0.6029 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6493 (tp30) cc_final: 0.6272 (pt0)
  outliers start: 23
  outliers final: 18
  residues processed: 88
  average time/residue: 0.2013
  time to fit residues: 23.9300
Evaluate side-chains
  82 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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  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   50 GLU
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  508 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0050
   chunk 93 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    1.4598

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

Flipped N/Q/H residues before XYZ refinement:
B 398 GLN
** B 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.179450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.156690 restraints weight = 13639.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.159487 restraints weight = 8616.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.160763 restraints weight = 5944.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6638
moved from start:          0.5602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7610  Z= 0.331
  Angle     :  0.729   9.291  10410  Z= 0.347
  Chirality :  0.046   0.193   1173
  Planarity :  0.006   0.040   1364
  Dihedral  :  6.910  81.545   1096
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 22.62 %
    Favored  : 74.21 %
  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: -1.21 (0.27), residues: 947
  helix: -0.61 (0.26), residues: 378
  sheet: -0.49 (0.36), residues: 192
  loop : -0.97 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 284 
 HIS   0.006   0.002   HIS A 335 
 PHE   0.020   0.003   PHE B 327 
 TYR   0.020   0.003   TYR A 307 
 ARG   0.011   0.001   ARG A 202 

*********************** 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
  99 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.846 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6949 (mtp180) cc_final: 0.5914 (tpt170)
REVERT: A  138 HIS cc_start: 0.7230 (OUTLIER) cc_final: 0.6403 (t-90)
REVERT: A  202 ARG cc_start: 0.6493 (mmp80) cc_final: 0.5953 (mmp80)
REVERT: B  355 PRO cc_start: 0.6195 (Cg_exo) cc_final: 0.5981 (Cg_endo)
  outliers start: 24
  outliers final: 22
  residues processed: 93
  average time/residue: 0.2110
  time to fit residues: 26.4864
Evaluate side-chains
  87 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
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  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  273 LEU
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   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  104 ASP
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  508 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 31 optimal weight:    0.0770
   chunk 22 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0970
   chunk 52 optimal weight:    0.0170
   chunk 34 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 92 optimal weight:    0.3980
   chunk 25 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.2374

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

Flipped N/Q/H residues before XYZ refinement:
B  57 ASN
B 398 GLN
B 410 GLN
B 513 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.186026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.162390 restraints weight = 13573.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.165745 restraints weight = 8288.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.167922 restraints weight = 5865.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6467
moved from start:          0.5645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7610  Z= 0.155
  Angle     :  0.607   9.623  10410  Z= 0.281
  Chirality :  0.041   0.210   1173
  Planarity :  0.005   0.042   1364
  Dihedral  :  6.006  69.642   1096
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 23.81 %
    Favored  : 73.02 %
  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: -0.63 (0.28), residues: 947
  helix: -0.12 (0.27), residues: 378
  sheet: -0.33 (0.37), residues: 190
  loop : -0.57 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 467 
 PHE   0.017   0.001   PHE B 327 
 TYR   0.016   0.001   TYR B 307 
 ARG   0.008   0.000   ARG A 202 

*********************** 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
  90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.620 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6079 (tpt170)
REVERT: A  138 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6340 (t-90)
REVERT: A  199 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7494 (tt)
REVERT: A  350 ASP cc_start: 0.6707 (p0) cc_final: 0.5996 (t70)
REVERT: A  376 TRP cc_start: 0.6091 (p-90) cc_final: 0.5001 (p-90)
  outliers start: 24
  outliers final: 16
  residues processed: 84
  average time/residue: 0.1989
  time to fit residues: 22.8180
Evaluate side-chains
  79 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  125 GLU
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  273 LEU
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  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   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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 88 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 94 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 116 HIS
B 241 GLN
B 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.176558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.154055 restraints weight = 13757.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.156064 restraints weight = 9049.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.157043 restraints weight = 6258.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6725
moved from start:          0.6122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   7610  Z= 0.410
  Angle     :  0.823   9.543  10410  Z= 0.395
  Chirality :  0.048   0.202   1173
  Planarity :  0.006   0.044   1364
  Dihedral  :  7.016  58.896   1096
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 24.34 %
    Favored  : 72.88 %
  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 (0.27), residues: 947
  helix: -0.87 (0.25), residues: 379
  sheet: -0.56 (0.36), residues: 200
  loop : -1.08 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 284 
 HIS   0.010   0.002   HIS A 344 
 PHE   0.018   0.003   PHE B 327 
 TYR   0.024   0.003   TYR A 472 
 ARG   0.006   0.001   ARG A 202 

********************** 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
  88 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6947 (mtp180) cc_final: 0.6081 (tpt170)
REVERT: A  138 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6144 (t-90)
REVERT: A  376 TRP cc_start: 0.6308 (p-90) cc_final: 0.5621 (p90)
REVERT: B  355 PRO cc_start: 0.6307 (Cg_exo) cc_final: 0.6105 (Cg_endo)
REVERT: B  357 LEU cc_start: 0.6014 (mp) cc_final: 0.5646 (mp)
REVERT: B  490 GLU cc_start: 0.6422 (mt-10) cc_final: 0.5974 (pt0)
  outliers start: 21
  outliers final: 18
  residues processed: 83
  average time/residue: 0.2089
  time to fit residues: 23.4949
Evaluate side-chains
  82 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  125 GLU
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  382 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
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  398 GLN
Chi-restraints excluded: chain B residue  479 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 91 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 67 optimal weight:    0.8980
   chunk 27 optimal weight:    0.4980
   chunk 59 optimal weight:    0.5980
   chunk 94 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 398 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.179818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.157252 restraints weight = 13500.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.159874 restraints weight = 8519.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.161003 restraints weight = 5906.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.4172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6630
moved from start:          0.6081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7610  Z= 0.218
  Angle     :  0.698   9.504  10410  Z= 0.330
  Chirality :  0.044   0.208   1173
  Planarity :  0.006   0.047   1364
  Dihedral  :  6.616  59.386   1096
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 24.60 %
    Favored  : 73.02 %
  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: -1.19 (0.27), residues: 947
  helix: -0.60 (0.26), residues: 380
  sheet: -0.51 (0.36), residues: 200
  loop : -0.93 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 284 
 HIS   0.005   0.001   HIS B 467 
 PHE   0.017   0.002   PHE B 327 
 TYR   0.017   0.002   TYR A 307 
 ARG   0.006   0.000   ARG A 202 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2531.96 seconds
wall clock time: 44 minutes 35.93 seconds (2675.93 seconds total)