Starting phenix.real_space_refine
on Fri Aug 22 20:20:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8avx_15686/08_2025/8avx_15686.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8avx_15686/08_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_15686/08_2025/8avx_15686.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8avx_15686/08_2025/8avx_15686.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8avx_15686/08_2025/8avx_15686.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8avx_15686/08_2025/8avx_15686.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.03, per 1000 atoms: 0.27
  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: 0.37
  Conformation dependent library (CDL) restraints added in 321.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.16
  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: 0.89

  Time building geometry restraints manager: 0.50 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 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:             7.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.680
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.0000

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

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

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.014   0.001   ARG A 100 
 TYR   0.030   0.003   TYR B 307 
 PHE   0.011   0.002   PHE B 170 
 TRP   0.017   0.002   TRP A 451 
 HIS   0.006   0.002   HIS A 349 

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

*********************** 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  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6840 (mtp180) cc_final: 0.5249 (tpt170)
REVERT: A  363 MET cc_start: 0.6975 (mmp) cc_final: 0.6549 (tpp)
REVERT: A  466 ARG cc_start: 0.4224 (OUTLIER) cc_final: 0.1648 (mmp80)
REVERT: B  227 THR cc_start: 0.7630 (p) cc_final: 0.7189 (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: 0.1135
  time to fit residues: 25.3533
Evaluate side-chains
  95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.0030
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  53 GLN
A 110 HIS
A 116 HIS
A 239 ASN
A 513 ASN
B 334 HIS
B 410 GLN
B 513 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.193834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.168598 restraints weight = 13266.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.172715 restraints weight = 7565.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.175340 restraints weight = 5123.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.177092 restraints weight = 3919.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.178224 restraints weight = 3249.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6237
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7610  Z= 0.125
  Angle     :  0.633   8.085  10410  Z= 0.300
  Chirality :  0.040   0.130   1173
  Planarity :  0.004   0.032   1364
  Dihedral  :  7.201  80.337   1103
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 16.40 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.46 (0.25), residues: 947
  helix: -2.02 (0.23), residues: 372
  sheet: -0.79 (0.36), residues: 193
  loop : -1.45 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 466 
 TYR   0.017   0.002   TYR A 479 
 PHE   0.019   0.002   PHE B 126 
 TRP   0.011   0.001   TRP A 284 
 HIS   0.007   0.001   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7610)
  covalent geometry    : angle       0.63304 (10410)
  hydrogen bonds       : bond        0.03752 (  322)
  hydrogen bonds       : angle       5.61141 (  906)

*********************** 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
  133 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6742 (mtp180) cc_final: 0.5728 (tpt170)
REVERT: A  466 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.1767 (mmt180)
REVERT: B   45 ASP cc_start: 0.5218 (t70) cc_final: 0.4953 (m-30)
REVERT: B  227 THR cc_start: 0.7052 (p) cc_final: 0.6798 (p)
REVERT: B  313 SER cc_start: 0.7746 (m) cc_final: 0.7531 (p)
REVERT: B  493 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7288 (t0)
  outliers start: 27
  outliers final: 6
  residues processed: 128
  average time/residue: 0.0905
  time to fit residues: 15.3249
Evaluate side-chains
  90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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  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  103 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 33 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0020
   chunk 43 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 93 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0170
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.1028

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

Flipped N/Q/H residues before XYZ refinement:
B  57 ASN
B 290 HIS
B 329 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 = 0.4448 r_free = 0.4448 target = 0.184758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.159702 restraints weight = 13549.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.163374 restraints weight = 8057.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.165800 restraints weight = 5638.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.167135 restraints weight = 4392.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.168337 restraints weight = 3737.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6476
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7610  Z= 0.174
  Angle     :  0.675   8.178  10410  Z= 0.325
  Chirality :  0.044   0.148   1173
  Planarity :  0.005   0.037   1364
  Dihedral  :  7.003  68.133   1098
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 18.12 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.25), residues: 947
  helix: -1.52 (0.25), residues: 372
  sheet: -0.59 (0.36), residues: 190
  loop : -1.19 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 172 
 TYR   0.018   0.002   TYR B 295 
 PHE   0.019   0.002   PHE B 327 
 TRP   0.022   0.002   TRP B 434 
 HIS   0.008   0.002   HIS B 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 7610)
  covalent geometry    : angle       0.67501 (10410)
  hydrogen bonds       : bond        0.04241 (  322)
  hydrogen bonds       : angle       5.46101 (  906)

*********************** 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
  117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 82
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6796 (mtp180) cc_final: 0.5770 (tpt170)
REVERT: A  202 ARG cc_start: 0.6407 (mmt90) cc_final: 0.5934 (mtt90)
REVERT: A  238 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7048 (mm)
REVERT: A  363 MET cc_start: 0.6346 (tpp) cc_final: 0.6134 (tpp)
REVERT: A  466 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.1670 (mmt180)
REVERT: B   45 ASP cc_start: 0.5486 (t70) cc_final: 0.5056 (m-30)
REVERT: B  355 PRO cc_start: 0.6660 (Cg_exo) cc_final: 0.6375 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6358 (tp30) cc_final: 0.6070 (pt0)
REVERT: B  441 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6275 (tp)
REVERT: B  493 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7228 (t0)
  outliers start: 35
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0794
  time to fit residues: 12.3105
Evaluate side-chains
  83 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  113 LEU
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  312 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  199 LEU
Chi-restraints excluded: chain B residue  232 VAL
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  441 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 50 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 79 optimal weight:    0.1980
   chunk 63 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 86 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.7780

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.185177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.160287 restraints weight = 13771.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.163891 restraints weight = 8186.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.166425 restraints weight = 5665.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.168054 restraints weight = 4384.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.168950 restraints weight = 3669.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6465
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      :  0.003   0.031   7610  Z= 0.136
  Angle     :  0.628   8.929  10410  Z= 0.293
  Chirality :  0.042   0.145   1173
  Planarity :  0.005   0.038   1364
  Dihedral  :  6.587  63.088   1098
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 19.58 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.26), residues: 947
  helix: -1.03 (0.26), residues: 381
  sheet: -0.60 (0.36), residues: 190
  loop : -0.99 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 446 
 TYR   0.012   0.002   TYR B 295 
 PHE   0.019   0.002   PHE B 327 
 TRP   0.019   0.001   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7610)
  covalent geometry    : angle       0.62798 (10410)
  hydrogen bonds       : bond        0.03595 (  322)
  hydrogen bonds       : angle       5.04718 (  906)

*********************** 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
  102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 72
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6823 (mtp180) cc_final: 0.5862 (tpt170)
REVERT: A  202 ARG cc_start: 0.6439 (mmt90) cc_final: 0.5927 (mtt90)
REVERT: A  466 ARG cc_start: 0.5286 (OUTLIER) cc_final: 0.1762 (mmt180)
REVERT: B   45 ASP cc_start: 0.5347 (t70) cc_final: 0.4948 (m-30)
REVERT: B  355 PRO cc_start: 0.6509 (Cg_exo) cc_final: 0.6249 (Cg_endo)
REVERT: B  432 GLU cc_start: 0.6531 (tp30) cc_final: 0.6316 (pt0)
REVERT: B  493 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7259 (t0)
  outliers start: 30
  outliers final: 19
  residues processed: 96
  average time/residue: 0.0884
  time to fit residues: 11.4425
Evaluate side-chains
  87 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  509 ILE
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  232 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  493 ASP
Chi-restraints excluded: chain B residue  508 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    0.1980
   chunk 39 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 260 HIS
A 266 ASN
B 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.184713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.161570 restraints weight = 13450.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.164081 restraints weight = 8724.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.165044 restraints weight = 6072.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.166611 restraints weight = 5137.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.166655 restraints weight = 4894.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.4234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.4830

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= 0.129
  Angle     :  0.615   9.000  10410  Z= 0.287
  Chirality :  0.042   0.179   1173
  Planarity :  0.005   0.038   1364
  Dihedral  :  6.565  81.305   1098
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 20.63 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.27), residues: 947
  helix: -0.67 (0.27), residues: 379
  sheet: -0.41 (0.37), residues: 185
  loop : -0.90 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 446 
 TYR   0.018   0.002   TYR A 263 
 PHE   0.021   0.002   PHE B 327 
 TRP   0.020   0.001   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7610)
  covalent geometry    : angle       0.61503 (10410)
  hydrogen bonds       : bond        0.03486 (  322)
  hydrogen bonds       : angle       4.89288 (  906)

*********************** 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
  105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 73
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6932 (mtp180) cc_final: 0.5802 (tpt170)
REVERT: A  466 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.1874 (mmt180)
REVERT: B   45 ASP cc_start: 0.5298 (t70) cc_final: 0.4898 (m-30)
REVERT: B  355 PRO cc_start: 0.6411 (Cg_exo) cc_final: 0.6170 (Cg_endo)
  outliers start: 32
  outliers final: 26
  residues processed: 97
  average time/residue: 0.0828
  time to fit residues: 10.8613
Evaluate side-chains
  93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  138 HIS
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  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  447 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  198 PHE
Chi-restraints excluded: chain B residue  199 LEU
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  378 THR
Chi-restraints excluded: chain B residue  398 GLN
Chi-restraints excluded: chain B residue  508 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 85 optimal weight:    0.4980
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 12 optimal weight:    0.0270
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 513 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.185086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.162192 restraints weight = 13501.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.164251 restraints weight = 8475.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.165490 restraints weight = 6259.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.165844 restraints weight = 5210.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.166771 restraints weight = 5009.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7610  Z= 0.110
  Angle     :  0.598   9.329  10410  Z= 0.276
  Chirality :  0.041   0.153   1173
  Planarity :  0.005   0.037   1364
  Dihedral  :  6.280  84.738   1096
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.27), residues: 947
  helix: -0.41 (0.27), residues: 378
  sheet: -0.43 (0.36), residues: 191
  loop : -0.76 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  70 
 TYR   0.023   0.002   TYR A 307 
 PHE   0.024   0.002   PHE B 327 
 TRP   0.022   0.001   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7610)
  covalent geometry    : angle       0.59838 (10410)
  hydrogen bonds       : bond        0.03191 (  322)
  hydrogen bonds       : angle       4.69965 (  906)

*********************** 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
  103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 72
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6871 (mtp180) cc_final: 0.5792 (tpt170)
REVERT: A  202 ARG cc_start: 0.6537 (mmt90) cc_final: 0.6187 (mtt90)
REVERT: B  105 TRP cc_start: 0.6235 (m-10) cc_final: 0.6001 (m-10)
REVERT: B  355 PRO cc_start: 0.6238 (Cg_exo) cc_final: 0.6020 (Cg_endo)
  outliers start: 31
  outliers final: 25
  residues processed: 93
  average time/residue: 0.0742
  time to fit residues: 9.2357
Evaluate side-chains
  92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
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  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  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   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  199 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  398 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    0.0170
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    5.9990
   chunk 55 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.6620

-------------------------------------------------------------------------------
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 = 0.4434 r_free = 0.4434 target = 0.183190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.160360 restraints weight = 13499.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.162937 restraints weight = 8483.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.163787 restraints weight = 5916.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.165406 restraints weight = 5043.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.165425 restraints weight = 4730.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.5334

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= 0.118
  Angle     :  0.598   9.443  10410  Z= 0.279
  Chirality :  0.041   0.144   1173
  Planarity :  0.005   0.038   1364
  Dihedral  :  6.373  87.230   1096
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.75 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.27), residues: 947
  helix: -0.27 (0.27), residues: 372
  sheet: -0.22 (0.37), residues: 186
  loop : -0.72 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  70 
 TYR   0.018   0.002   TYR A 307 
 PHE   0.021   0.002   PHE B 327 
 TRP   0.022   0.001   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7610)
  covalent geometry    : angle       0.59847 (10410)
  hydrogen bonds       : bond        0.03289 (  322)
  hydrogen bonds       : angle       4.71936 (  906)

*********************** 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
  98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6949 (mtp180) cc_final: 0.5947 (tpt170)
REVERT: B  355 PRO cc_start: 0.6239 (Cg_exo) cc_final: 0.6018 (Cg_endo)
  outliers start: 31
  outliers final: 28
  residues processed: 91
  average time/residue: 0.0831
  time to fit residues: 10.3438
Evaluate side-chains
  90 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 62
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  138 HIS
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  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  430 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   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  199 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  398 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 40 optimal weight:    4.9990
   chunk 94 optimal weight:    0.8980
   chunk 15 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.4445 r_free = 0.4445 target = 0.184081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.161474 restraints weight = 13668.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.164279 restraints weight = 8262.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.165635 restraints weight = 5745.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.166493 restraints weight = 4736.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.166705 restraints weight = 4678.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.5519

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= 0.112
  Angle     :  0.599   9.636  10410  Z= 0.277
  Chirality :  0.041   0.169   1173
  Planarity :  0.005   0.038   1364
  Dihedral  :  6.323  89.270   1096
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 23.68 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.27), residues: 947
  helix: -0.16 (0.27), residues: 376
  sheet: -0.19 (0.37), residues: 186
  loop : -0.71 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 202 
 TYR   0.017   0.002   TYR A 307 
 PHE   0.020   0.001   PHE B 327 
 TRP   0.023   0.001   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7610)
  covalent geometry    : angle       0.59870 (10410)
  hydrogen bonds       : bond        0.03178 (  322)
  hydrogen bonds       : angle       4.60511 (  906)

*********************** 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
  97 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6988 (mtp180) cc_final: 0.6044 (tpt170)
REVERT: A  138 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6324 (t-90)
REVERT: A  199 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7490 (tt)
REVERT: A  474 GLU cc_start: 0.3342 (tp30) cc_final: 0.2637 (mt-10)
REVERT: B  398 GLN cc_start: 0.3052 (OUTLIER) cc_final: 0.2847 (tp40)
  outliers start: 30
  outliers final: 23
  residues processed: 90
  average time/residue: 0.0897
  time to fit residues: 10.8810
Evaluate side-chains
  82 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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  187 ILE
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  430 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   77 LEU
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  223 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  378 THR
Chi-restraints excluded: chain B residue  398 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 87 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 90 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.181710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.158061 restraints weight = 13402.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.161252 restraints weight = 8166.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.163440 restraints weight = 5771.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.164620 restraints weight = 4562.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.165765 restraints weight = 3910.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.5690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7610  Z= 0.133
  Angle     :  0.638   9.702  10410  Z= 0.298
  Chirality :  0.042   0.193   1173
  Planarity :  0.005   0.040   1364
  Dihedral  :  6.423  89.875   1096
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 23.41 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.27), residues: 947
  helix: -0.22 (0.27), residues: 377
  sheet: -0.10 (0.38), residues: 186
  loop : -0.75 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 202 
 TYR   0.031   0.002   TYR A 263 
 PHE   0.019   0.002   PHE B 327 
 TRP   0.023   0.002   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7610)
  covalent geometry    : angle       0.63830 (10410)
  hydrogen bonds       : bond        0.03517 (  322)
  hydrogen bonds       : angle       4.69995 (  906)

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

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 61
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   26 ARG cc_start: 0.6915 (mtp180) cc_final: 0.6136 (tpt170)
REVERT: A  138 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6220 (t-90)
REVERT: A  202 ARG cc_start: 0.6459 (mmp80) cc_final: 0.6189 (mmp80)
  outliers start: 31
  outliers final: 25
  residues processed: 84
  average time/residue: 0.0867
  time to fit residues: 9.6907
Evaluate side-chains
  85 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  138 HIS
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  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  430 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   77 LEU
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  223 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0870
   chunk 80 optimal weight:    0.5980
   chunk 26 optimal weight:    0.1980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.4558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.183828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.160317 restraints weight = 13527.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.163655 restraints weight = 8144.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.165880 restraints weight = 5711.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.167384 restraints weight = 4469.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.168203 restraints weight = 3760.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6464
moved from start:          0.5781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7610  Z= 0.105
  Angle     :  0.607   9.942  10410  Z= 0.279
  Chirality :  0.041   0.181   1173
  Planarity :  0.005   0.044   1364
  Dihedral  :  5.805  63.772   1096
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 23.81 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.28), residues: 947
  helix:  0.01 (0.28), residues: 376
  sheet: -0.08 (0.38), residues: 185
  loop : -0.64 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 202 
 TYR   0.018   0.002   TYR A 307 
 PHE   0.018   0.001   PHE B 327 
 TRP   0.043   0.001   TRP A 284 
 HIS   0.004   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7610)
  covalent geometry    : angle       0.60731 (10410)
  hydrogen bonds       : bond        0.03052 (  322)
  hydrogen bonds       : angle       4.50515 (  906)

********************** 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
  86 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 60
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   26 ARG cc_start: 0.6928 (mtp180) cc_final: 0.6150 (tpt170)
REVERT: A  138 HIS cc_start: 0.7013 (OUTLIER) cc_final: 0.6247 (t-90)
REVERT: A  202 ARG cc_start: 0.6201 (mmp80) cc_final: 0.5906 (mmp80)
REVERT: A  306 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7251 (mp0)
REVERT: A  474 GLU cc_start: 0.3247 (tp30) cc_final: 0.2621 (mp0)
  outliers start: 26
  outliers final: 21
  residues processed: 81
  average time/residue: 0.0913
  time to fit residues: 9.8828
Evaluate side-chains
  80 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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  187 ILE
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  441 LEU
Chi-restraints excluded: chain A residue  449 VAL
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   50 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   77 LEU
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  223 LEU
Chi-restraints excluded: chain B residue  237 VAL
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  378 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 95 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.4407 r_free = 0.4407 target = 0.180495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.157139 restraints weight = 13519.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.160122 restraints weight = 8412.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.162264 restraints weight = 5999.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.163726 restraints weight = 4753.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.164524 restraints weight = 4029.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.4225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.5998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7610  Z= 0.143
  Angle     :  0.650   9.630  10410  Z= 0.304
  Chirality :  0.043   0.182   1173
  Planarity :  0.005   0.045   1364
  Dihedral  :  6.245  61.926   1096
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 24.21 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.27), residues: 947
  helix: -0.14 (0.27), residues: 376
  sheet: -0.12 (0.38), residues: 187
  loop : -0.78 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 202 
 TYR   0.014   0.002   TYR B 295 
 PHE   0.019   0.002   PHE B 327 
 TRP   0.034   0.002   TRP A 284 
 HIS   0.005   0.001   HIS B 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 7610)
  covalent geometry    : angle       0.64953 (10410)
  hydrogen bonds       : bond        0.03664 (  322)
  hydrogen bonds       : angle       4.78652 (  906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1402.61 seconds
wall clock time: 24 minutes 49.56 seconds (1489.56 seconds total)