Starting phenix.real_space_refine
on Wed Feb 12 21:40:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r8c_24315/02_2025/7r8c_24315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8c_24315/02_2025/7r8c_24315.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r8c_24315/02_2025/7r8c_24315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8c_24315/02_2025/7r8c_24315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8c_24315/02_2025/7r8c_24315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8c_24315/02_2025/7r8c_24315.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.002
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      68      5.16       5
     C    5540      2.51       5
     N    1412      2.21       5
     O    1518      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8538
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4269
          Classifications: {'peptide': 545}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4269
          Classifications: {'peptide': 545}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 2
  Time building chain proxies: 5.19, per 1000 atoms: 0.61
  Number of scatterers: 8538
  At special positions: 0
  Unit cell: (107.457, 75.803, 119.952, 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      68     16.00
     O    1518      8.00
     N    1412      7.00
     C    5540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 611 " - pdb=" SG  CYS A 617 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 611 " - pdb=" SG  CYS B 617 " distance=2.03

  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: 2.27
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2016

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      63.3% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 132
      removed outlier: 3.613A  pdb=" N   MET A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 158
      removed outlier: 3.699A  pdb=" N   LYS A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A 158 " --> pdb=" O   CYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 186
    Processing helix  chain 'A' and resid 189 through 205
    Processing helix  chain 'A' and resid 206 through 210
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 218 through 230
    Processing helix  chain 'A' and resid 248 through 265
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.840A  pdb=" N   LEU A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 303
    Processing helix  chain 'A' and resid 304 through 311
      removed outlier: 3.642A  pdb=" N   LEU A 311 " --> pdb=" O   TYR A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.740A  pdb=" N   ASP A 407 " --> pdb=" O   SER A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 429
      removed outlier: 3.611A  pdb=" N   ILE A 415 " --> pdb=" O   THR A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 465
      removed outlier: 3.624A  pdb=" N   PHE A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      Proline residue:  A 460  - end of helix
    Processing helix  chain 'A' and resid 469 through 478
      removed outlier: 3.706A  pdb=" N   ASN A 478 " --> pdb=" O   ARG A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 511
      Proline residue:  A 496  - end of helix
      Proline residue:  A 502  - end of helix
      removed outlier: 3.854A  pdb=" N   TRP A 511 " --> pdb=" O   SER A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 547
    Processing helix  chain 'A' and resid 549 through 567
      Proline residue:  A 558  - end of helix
      Proline residue:  A 563  - end of helix
      removed outlier: 3.630A  pdb=" N   LEU A 566 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.788A  pdb=" N   ILE A 587 " --> pdb=" O   TRP A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 602
      removed outlier: 3.551A  pdb=" N   TYR A 592 " --> pdb=" O   SER A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 622
      removed outlier: 4.294A  pdb=" N   SER A 622 " --> pdb=" O   PHE A 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 619 through 622'
    Processing helix  chain 'A' and resid 623 through 629
    Processing helix  chain 'A' and resid 635 through 665
      removed outlier: 3.888A  pdb=" N   ASP A 639 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 132
      removed outlier: 3.614A  pdb=" N   MET B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 158
      removed outlier: 3.700A  pdb=" N   LYS B 157 " --> pdb=" O   ARG B 153 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 186
    Processing helix  chain 'B' and resid 189 through 205
    Processing helix  chain 'B' and resid 206 through 210
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 218 through 230
    Processing helix  chain 'B' and resid 248 through 265
    Processing helix  chain 'B' and resid 277 through 283
      removed outlier: 3.840A  pdb=" N   LEU B 283 " --> pdb=" O   LYS B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 303
    Processing helix  chain 'B' and resid 304 through 311
      removed outlier: 3.640A  pdb=" N   LEU B 311 " --> pdb=" O   TYR B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
    Processing helix  chain 'B' and resid 336 through 346
    Processing helix  chain 'B' and resid 390 through 407
      removed outlier: 3.739A  pdb=" N   ASP B 407 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 429
      removed outlier: 3.610A  pdb=" N   ILE B 415 " --> pdb=" O   THR B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 465
      removed outlier: 3.624A  pdb=" N   PHE B 448 " --> pdb=" O   GLY B 444 " (cutoff:3.500A)
      Proline residue:  B 460  - end of helix
    Processing helix  chain 'B' and resid 469 through 478
      removed outlier: 3.707A  pdb=" N   ASN B 478 " --> pdb=" O   ARG B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 511
      Proline residue:  B 496  - end of helix
      Proline residue:  B 502  - end of helix
      removed outlier: 3.855A  pdb=" N   TRP B 511 " --> pdb=" O   SER B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 547
    Processing helix  chain 'B' and resid 549 through 567
      Proline residue:  B 558  - end of helix
      Proline residue:  B 563  - end of helix
      removed outlier: 3.630A  pdb=" N   LEU B 566 " --> pdb=" O   ILE B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 587
      removed outlier: 3.788A  pdb=" N   ILE B 587 " --> pdb=" O   TRP B 583 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 602
      removed outlier: 3.551A  pdb=" N   TYR B 592 " --> pdb=" O   SER B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 622
      removed outlier: 4.295A  pdb=" N   SER B 622 " --> pdb=" O   PHE B 619 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 619 through 622'
    Processing helix  chain 'B' and resid 623 through 629
    Processing helix  chain 'B' and resid 635 through 665
      removed outlier: 3.888A  pdb=" N   ASP B 639 " --> pdb=" O   LYS B 635 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108
      removed outlier: 5.375A  pdb=" N   LYS A 102 " --> pdb=" O   TYR A  84 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   TYR A  84 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   GLY A 106 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   ARG A  80 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE A 108 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLU A  78 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A  80 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 142 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162
      removed outlier: 6.159A  pdb=" N   MET A 238 " --> pdb=" O   ILE A 270 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   THR A 272 " --> pdb=" O   MET A 238 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   PHE A 240 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU A 113 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   TYR A 288 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ALA A 115 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   LEU A 290 " --> pdb=" O   ALA A 115 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   MET A 117 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU A 287 " --> pdb=" O   ARG A 298 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   ARG A 298 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 289 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 108
      removed outlier: 5.374A  pdb=" N   LYS B 102 " --> pdb=" O   TYR B  84 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   TYR B  84 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   GLY B 106 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   ARG B  80 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   PHE B 108 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLU B  78 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG B  80 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ALA B 142 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162
      removed outlier: 6.159A  pdb=" N   MET B 238 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   THR B 272 " --> pdb=" O   MET B 238 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   PHE B 240 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      removed outlier: 6.764A  pdb=" N   LEU B 113 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   TYR B 288 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ALA B 115 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   LEU B 290 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   MET B 117 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   LEU B 287 " --> pdb=" O   ARG B 298 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ARG B 298 " --> pdb=" O   LEU B 287 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2688
        1.34 -     1.46: 1765
        1.46 -     1.58: 4151
        1.58 -     1.69: 0
        1.69 -     1.81: 110
  Bond restraints: 8714
  Sorted by residual:
  bond pdb=" C   ILE B 562 "
       pdb=" N   PRO B 563 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.25e-02 6.40e+03 3.26e+00
  bond pdb=" C   ILE A 562 "
       pdb=" N   PRO A 563 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.023 1.25e-02 6.40e+03 3.25e+00
  bond pdb=" C   PHE B 465 "
       pdb=" N   PRO B 466 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.05e+00
  bond pdb=" C   PHE A 465 "
       pdb=" N   PRO A 466 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 1.01e+00
  bond pdb=" N   VAL B 631 "
       pdb=" CA  VAL B 631 "
    ideal  model  delta    sigma   weight residual
    1.474  1.461  0.013 1.57e-02 4.06e+03 7.11e-01
  ... (remaining 8709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.08: 11352
        1.08 -     2.16: 335
        2.16 -     3.25: 57
        3.25 -     4.33: 20
        4.33 -     5.41: 14
  Bond angle restraints: 11778
  Sorted by residual:
  angle pdb=" C   GLN A 620 "
        pdb=" N   LYS A 621 "
        pdb=" CA  LYS A 621 "
      ideal   model   delta    sigma   weight residual
     123.91  129.10   -5.19 1.66e+00 3.63e-01 9.76e+00
  angle pdb=" C   GLN B 620 "
        pdb=" N   LYS B 621 "
        pdb=" CA  LYS B 621 "
      ideal   model   delta    sigma   weight residual
     123.91  129.09   -5.18 1.66e+00 3.63e-01 9.73e+00
  angle pdb=" N   PHE B 571 "
        pdb=" CA  PHE B 571 "
        pdb=" C   PHE B 571 "
      ideal   model   delta    sigma   weight residual
     114.04  110.76    3.28 1.24e+00 6.50e-01 6.98e+00
  angle pdb=" N   PHE A 571 "
        pdb=" CA  PHE A 571 "
        pdb=" C   PHE A 571 "
      ideal   model   delta    sigma   weight residual
     114.04  110.81    3.23 1.24e+00 6.50e-01 6.80e+00
  angle pdb=" C   ILE B 562 "
        pdb=" CA  ILE B 562 "
        pdb=" CB  ILE B 562 "
      ideal   model   delta    sigma   weight residual
     114.00  110.64    3.36 1.31e+00 5.83e-01 6.56e+00
  ... (remaining 11773 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.47: 4579
       14.47 -    28.94: 444
       28.94 -    43.41: 130
       43.41 -    57.88: 31
       57.88 -    72.35: 6
  Dihedral angle restraints: 5190
    sinusoidal: 2044
      harmonic: 3146
  Sorted by residual:
  dihedral pdb=" CA  ASP A 323 "
           pdb=" CB  ASP A 323 "
           pdb=" CG  ASP A 323 "
           pdb=" OD1 ASP A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.71   53.71     1      2.00e+01 2.50e-03 9.79e+00
  dihedral pdb=" CA  ASP B 323 "
           pdb=" CB  ASP B 323 "
           pdb=" CG  ASP B 323 "
           pdb=" OD1 ASP B 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.70   53.70     1      2.00e+01 2.50e-03 9.79e+00
  dihedral pdb=" CA  PRO A 466 "
           pdb=" C   PRO A 466 "
           pdb=" N   LEU A 467 "
           pdb=" CA  LEU A 467 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.81   15.19     0      5.00e+00 4.00e-02 9.23e+00
  ... (remaining 5187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 862
       0.027 -    0.055: 312
       0.055 -    0.082: 113
       0.082 -    0.110: 54
       0.110 -    0.137: 15
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CA  ILE B 577 "
            pdb=" N   ILE B 577 "
            pdb=" C   ILE B 577 "
            pdb=" CB  ILE B 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.70e-01
  chirality pdb=" CA  ILE A 577 "
            pdb=" N   ILE A 577 "
            pdb=" C   ILE A 577 "
            pdb=" CB  ILE A 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  LYS B 621 "
            pdb=" N   LYS B 621 "
            pdb=" C   LYS B 621 "
            pdb=" CB  LYS B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1353 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 456 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.53e+00
        pdb=" C   ALA B 456 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ALA B 456 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B 457 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 456 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.48e+00
        pdb=" C   ALA A 456 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ALA A 456 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 457 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 465 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO B 466 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B 466 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 466 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 82
        2.64 -     3.20: 7866
        3.20 -     3.77: 13030
        3.77 -     4.33: 17371
        4.33 -     4.90: 29252
  Nonbonded interactions: 67601
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU A 231 "
            pdb=" NH1 ARG A 267 "
     model   vdw
     2.073 3.540
  nonbonded pdb=" OE1 GLU A 475 "
            pdb=" OH  TYR A 481 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OE1 GLU B 475 "
            pdb=" OH  TYR B 481 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   ILE A 404 "
            pdb=" OG1 THR A 411 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   ILE B 404 "
            pdb=" OG1 THR B 411 "
     model   vdw
     2.250 3.040
  ... (remaining 67596 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.800
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
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      :  0.002   0.024   8714  Z= 0.116
  Angle     :  0.494   5.412  11778  Z= 0.296
  Chirality :  0.037   0.137   1356
  Planarity :  0.003   0.034   1474
  Dihedral  : 12.820  72.351   3168
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.43 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.24), residues: 1078
  helix: -0.12 (0.20), residues: 630
  sheet: -1.34 (0.47), residues: 80
  loop : -2.66 (0.30), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 511 
 HIS   0.001   0.000   HIS A 171 
 PHE   0.006   0.001   PHE B 646 
 TYR   0.006   0.001   TYR A 510 
 ARG   0.001   0.000   ARG A 651 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 211
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.8611 (t80) cc_final: 0.8353 (t80)
REVERT: A  178 MET cc_start: 0.9440 (mmm) cc_final: 0.9233 (mmm)
REVERT: A  213 ARG cc_start: 0.8762 (mmt90) cc_final: 0.8488 (mmt90)
REVERT: A  230 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8416 (mm-30)
REVERT: A  238 MET cc_start: 0.8362 (mtp) cc_final: 0.8083 (mtp)
REVERT: A  500 MET cc_start: 0.8232 (tmm) cc_final: 0.7463 (tmm)
REVERT: A  511 TRP cc_start: 0.8076 (m100) cc_final: 0.7498 (t60)
REVERT: A  592 TYR cc_start: 0.8795 (m-80) cc_final: 0.8483 (m-80)
REVERT: A  595 GLU cc_start: 0.8259 (tt0) cc_final: 0.8048 (tt0)
REVERT: A  611 CYS cc_start: 0.4162 (t) cc_final: 0.3905 (t)
REVERT: A  628 GLU cc_start: 0.8938 (tp30) cc_final: 0.8697 (tp30)
REVERT: B  155 PHE cc_start: 0.8698 (t80) cc_final: 0.8400 (t80)
REVERT: B  176 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8261 (mt-10)
REVERT: B  178 MET cc_start: 0.9424 (mmm) cc_final: 0.9210 (mmm)
REVERT: B  213 ARG cc_start: 0.8761 (mmt90) cc_final: 0.8489 (mmt90)
REVERT: B  230 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8414 (mm-30)
REVERT: B  238 MET cc_start: 0.8378 (mtp) cc_final: 0.8091 (mtp)
REVERT: B  500 MET cc_start: 0.8241 (tmm) cc_final: 0.7460 (tmm)
REVERT: B  511 TRP cc_start: 0.8130 (m100) cc_final: 0.7511 (t60)
REVERT: B  570 PHE cc_start: 0.8335 (t80) cc_final: 0.7753 (t80)
REVERT: B  592 TYR cc_start: 0.8780 (m-80) cc_final: 0.8402 (m-80)
REVERT: B  595 GLU cc_start: 0.8252 (tt0) cc_final: 0.8047 (tt0)
REVERT: B  611 CYS cc_start: 0.4166 (t) cc_final: 0.3958 (t)
REVERT: B  628 GLU cc_start: 0.8968 (tp30) cc_final: 0.8736 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2003
  time to fit residues: 58.9695
Evaluate side-chains
  127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.0970
   chunk 81 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
A 264 GLN
A 336 GLN
A 476 HIS
B 221 GLN
B 264 GLN
B 336 GLN
B 476 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.097047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.080714 restraints weight = 16534.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.083786 restraints weight = 8166.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.085925 restraints weight = 5027.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   8714  Z= 0.313
  Angle     :  0.613   8.683  11778  Z= 0.304
  Chirality :  0.042   0.153   1356
  Planarity :  0.004   0.036   1474
  Dihedral  :  3.682  18.172   1188
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.12 %
    Favored  : 85.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.26), residues: 1078
  helix:  1.22 (0.21), residues: 640
  sheet: -0.83 (0.47), residues: 82
  loop : -2.20 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 480 
 HIS   0.010   0.002   HIS A 171 
 PHE   0.021   0.002   PHE A 281 
 TYR   0.011   0.001   TYR B 510 
 ARG   0.004   0.001   ARG B 651 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 125
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.9047 (t80) cc_final: 0.8747 (t80)
REVERT: A  213 ARG cc_start: 0.8794 (mmt90) cc_final: 0.8468 (mmt90)
REVERT: A  454 MET cc_start: 0.8772 (ppp) cc_final: 0.8563 (tmm)
REVERT: A  500 MET cc_start: 0.8195 (tmm) cc_final: 0.7468 (tmm)
REVERT: A  511 TRP cc_start: 0.8146 (m100) cc_final: 0.7628 (t60)
REVERT: A  592 TYR cc_start: 0.8824 (m-80) cc_final: 0.8598 (m-10)
REVERT: A  595 GLU cc_start: 0.8263 (tt0) cc_final: 0.7961 (tt0)
REVERT: A  628 GLU cc_start: 0.8880 (tp30) cc_final: 0.8652 (tp30)
REVERT: B  155 PHE cc_start: 0.9032 (t80) cc_final: 0.8720 (t80)
REVERT: B  178 MET cc_start: 0.9472 (mmm) cc_final: 0.9270 (mmm)
REVERT: B  213 ARG cc_start: 0.8796 (mmt90) cc_final: 0.8470 (mmt90)
REVERT: B  500 MET cc_start: 0.8198 (tmm) cc_final: 0.7479 (tmm)
REVERT: B  511 TRP cc_start: 0.8124 (m100) cc_final: 0.7629 (t60)
REVERT: B  592 TYR cc_start: 0.8825 (m-80) cc_final: 0.8531 (m-80)
REVERT: B  595 GLU cc_start: 0.8239 (tt0) cc_final: 0.7943 (tt0)
REVERT: B  628 GLU cc_start: 0.8903 (tp30) cc_final: 0.8684 (tp30)
  outliers start: 18
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1854
  time to fit residues: 35.5326
Evaluate side-chains
  130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  645 ILE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  645 ILE
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 87 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0370
   chunk 24 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.098362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.081977 restraints weight = 16639.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.085129 restraints weight = 8101.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.087311 restraints weight = 4939.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8714  Z= 0.149
  Angle     :  0.511   6.047  11778  Z= 0.254
  Chirality :  0.039   0.144   1356
  Planarity :  0.003   0.037   1474
  Dihedral  :  3.589  18.705   1188
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.52 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.27), residues: 1078
  helix:  1.70 (0.21), residues: 638
  sheet: -0.97 (0.45), residues: 82
  loop : -1.95 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 480 
 HIS   0.008   0.001   HIS A 171 
 PHE   0.017   0.001   PHE A 281 
 TYR   0.008   0.001   TYR A 580 
 ARG   0.002   0.000   ARG B 591 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.9042 (t80) cc_final: 0.8721 (t80)
REVERT: A  179 MET cc_start: 0.9074 (mmm) cc_final: 0.8720 (mmm)
REVERT: A  500 MET cc_start: 0.8244 (tmm) cc_final: 0.7538 (tmm)
REVERT: A  595 GLU cc_start: 0.8224 (tt0) cc_final: 0.7970 (tt0)
REVERT: A  628 GLU cc_start: 0.8816 (tp30) cc_final: 0.8454 (tp30)
REVERT: B  155 PHE cc_start: 0.9038 (t80) cc_final: 0.8711 (t80)
REVERT: B  178 MET cc_start: 0.9479 (mmm) cc_final: 0.9260 (mmm)
REVERT: B  179 MET cc_start: 0.9085 (mmm) cc_final: 0.8759 (mmm)
REVERT: B  500 MET cc_start: 0.8265 (tmm) cc_final: 0.7552 (tmm)
REVERT: B  511 TRP cc_start: 0.8118 (m100) cc_final: 0.7559 (t60)
REVERT: B  595 GLU cc_start: 0.8242 (tt0) cc_final: 0.8023 (tt0)
REVERT: B  628 GLU cc_start: 0.8845 (tp30) cc_final: 0.8506 (tp30)
  outliers start: 23
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1907
  time to fit residues: 38.9138
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 104 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.2980
   chunk 90 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    2.2588

-------------------------------------------------------------------------------
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 = 0.3273 r_free = 0.3273 target = 0.093857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.076796 restraints weight = 16834.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.079887 restraints weight = 8199.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.082043 restraints weight = 5038.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8714  Z= 0.307
  Angle     :  0.580   5.698  11778  Z= 0.292
  Chirality :  0.041   0.163   1356
  Planarity :  0.004   0.039   1474
  Dihedral  :  3.758  20.534   1188
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 15.77 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.27), residues: 1078
  helix:  1.60 (0.21), residues: 656
  sheet: -0.96 (0.48), residues: 82
  loop : -1.85 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 480 
 HIS   0.009   0.001   HIS B 171 
 PHE   0.014   0.002   PHE B 448 
 TYR   0.025   0.001   TYR B 592 
 ARG   0.003   0.000   ARG B 651 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  179 MET cc_start: 0.9030 (mmm) cc_final: 0.8666 (mmm)
REVERT: A  500 MET cc_start: 0.8242 (tmm) cc_final: 0.7535 (tmm)
REVERT: A  628 GLU cc_start: 0.8838 (tp30) cc_final: 0.8383 (tm-30)
REVERT: B  179 MET cc_start: 0.9017 (mmm) cc_final: 0.8685 (mmm)
REVERT: B  500 MET cc_start: 0.8220 (tmm) cc_final: 0.7499 (tmm)
REVERT: B  512 MET cc_start: 0.9071 (ttm) cc_final: 0.8788 (ttt)
REVERT: B  628 GLU cc_start: 0.8851 (tp30) cc_final: 0.8550 (tp30)
  outliers start: 30
  outliers final: 22
  residues processed: 128
  average time/residue: 0.1784
  time to fit residues: 33.3810
Evaluate side-chains
  129 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 56 optimal weight:   10.0000
   chunk 80 optimal weight:    0.2980
   chunk 49 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3313 r_free = 0.3313 target = 0.096316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.079501 restraints weight = 16450.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.082631 restraints weight = 8219.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.084727 restraints weight = 5097.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8714  Z= 0.145
  Angle     :  0.515   6.998  11778  Z= 0.257
  Chirality :  0.039   0.160   1356
  Planarity :  0.003   0.040   1474
  Dihedral  :  3.637  20.055   1188
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.38 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 1078
  helix:  1.82 (0.21), residues: 656
  sheet: -0.80 (0.50), residues: 82
  loop : -1.72 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 480 
 HIS   0.007   0.001   HIS B 171 
 PHE   0.013   0.001   PHE A 281 
 TYR   0.019   0.001   TYR A 592 
 ARG   0.002   0.000   ARG A 213 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8872 (mmm) cc_final: 0.8609 (mmm)
REVERT: A  500 MET cc_start: 0.8260 (tmm) cc_final: 0.7602 (tmm)
REVERT: A  628 GLU cc_start: 0.8674 (tp30) cc_final: 0.8264 (tm-30)
REVERT: B  179 MET cc_start: 0.8889 (mmm) cc_final: 0.8638 (mmm)
REVERT: B  500 MET cc_start: 0.8250 (tmm) cc_final: 0.7607 (tmm)
REVERT: B  512 MET cc_start: 0.8955 (ttm) cc_final: 0.8706 (ttt)
REVERT: B  628 GLU cc_start: 0.8698 (tp30) cc_final: 0.8398 (tp30)
  outliers start: 23
  outliers final: 18
  residues processed: 129
  average time/residue: 0.1701
  time to fit residues: 32.6819
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    0.4980
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 86 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 91 optimal weight:    0.0370
   chunk 89 optimal weight:    4.9990
   chunk 43 optimal weight:    0.4980
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3355 r_free = 0.3355 target = 0.099272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.082802 restraints weight = 16239.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.085975 restraints weight = 7959.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.088170 restraints weight = 4880.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.2533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.054   8714  Z= 0.133
  Angle     :  0.523   7.021  11778  Z= 0.257
  Chirality :  0.039   0.178   1356
  Planarity :  0.003   0.040   1474
  Dihedral  :  3.522  18.948   1188
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.60 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 1078
  helix:  1.99 (0.21), residues: 654
  sheet: -0.67 (0.51), residues: 82
  loop : -1.60 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 480 
 HIS   0.008   0.001   HIS B 618 
 PHE   0.013   0.001   PHE B 281 
 TYR   0.014   0.001   TYR A 592 
 ARG   0.005   0.000   ARG B 345 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8840 (mmm) cc_final: 0.8613 (mmm)
REVERT: A  500 MET cc_start: 0.8252 (tmm) cc_final: 0.7592 (tmm)
REVERT: A  628 GLU cc_start: 0.8616 (tp30) cc_final: 0.8117 (tm-30)
REVERT: B  179 MET cc_start: 0.8845 (mmm) cc_final: 0.8609 (mmm)
REVERT: B  500 MET cc_start: 0.8263 (tmm) cc_final: 0.7620 (tmm)
REVERT: B  628 GLU cc_start: 0.8638 (tp30) cc_final: 0.8336 (tp30)
  outliers start: 26
  outliers final: 22
  residues processed: 137
  average time/residue: 0.1732
  time to fit residues: 35.2720
Evaluate side-chains
  131 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0570
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    0.2980
   chunk 92 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.8702

-------------------------------------------------------------------------------
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 = 0.3331 r_free = 0.3331 target = 0.097403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.080728 restraints weight = 16443.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.083903 restraints weight = 8164.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.086076 restraints weight = 5037.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8714  Z= 0.165
  Angle     :  0.558  11.037  11778  Z= 0.275
  Chirality :  0.039   0.207   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.648  27.454   1188
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.81 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.27), residues: 1078
  helix:  2.02 (0.21), residues: 656
  sheet: -0.65 (0.51), residues: 82
  loop : -1.57 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 583 
 HIS   0.013   0.001   HIS B 618 
 PHE   0.012   0.001   PHE B 281 
 TYR   0.014   0.001   TYR A 592 
 ARG   0.002   0.000   ARG B 345 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 115
  time to evaluate  : 1.224 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8951 (mmm) cc_final: 0.8683 (mmm)
REVERT: A  500 MET cc_start: 0.8260 (tmm) cc_final: 0.7573 (tmm)
REVERT: A  628 GLU cc_start: 0.8713 (tp30) cc_final: 0.8171 (tm-30)
REVERT: B  179 MET cc_start: 0.9006 (mmm) cc_final: 0.8713 (mmm)
REVERT: B  500 MET cc_start: 0.8266 (tmm) cc_final: 0.7598 (tmm)
REVERT: B  628 GLU cc_start: 0.8746 (tp30) cc_final: 0.8428 (tp30)
  outliers start: 26
  outliers final: 25
  residues processed: 127
  average time/residue: 0.1664
  time to fit residues: 32.0811
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 104 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3315 r_free = 0.3315 target = 0.096432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.079855 restraints weight = 16746.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.082969 restraints weight = 8277.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.085137 restraints weight = 5104.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8714  Z= 0.207
  Angle     :  0.565   7.890  11778  Z= 0.277
  Chirality :  0.040   0.245   1356
  Planarity :  0.003   0.043   1474
  Dihedral  :  3.642  19.647   1188
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.45 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.27), residues: 1078
  helix:  2.08 (0.21), residues: 656
  sheet: -0.74 (0.51), residues: 82
  loop : -1.52 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 511 
 HIS   0.012   0.001   HIS B 618 
 PHE   0.015   0.001   PHE A 284 
 TYR   0.015   0.001   TYR A 592 
 ARG   0.002   0.000   ARG B 651 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8778 (mmm) cc_final: 0.8551 (mmm)
REVERT: A  500 MET cc_start: 0.8247 (tmm) cc_final: 0.7636 (tmm)
REVERT: A  628 GLU cc_start: 0.8638 (tp30) cc_final: 0.8121 (tm-30)
REVERT: B  179 MET cc_start: 0.8849 (mmm) cc_final: 0.8614 (mmm)
REVERT: B  500 MET cc_start: 0.8293 (tmm) cc_final: 0.7664 (tmm)
REVERT: B  628 GLU cc_start: 0.8644 (tp30) cc_final: 0.8340 (tp30)
  outliers start: 26
  outliers final: 24
  residues processed: 125
  average time/residue: 0.1679
  time to fit residues: 31.7177
Evaluate side-chains
  130 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  560 THR
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain A residue  617 CYS
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  590 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 64 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0270
   chunk 48 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.3346 r_free = 0.3346 target = 0.098229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.081669 restraints weight = 16490.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.084832 restraints weight = 8183.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.087049 restraints weight = 5039.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8714  Z= 0.145
  Angle     :  0.577   9.474  11778  Z= 0.277
  Chirality :  0.040   0.303   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.688  25.800   1188
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.78 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.27), residues: 1078
  helix:  2.12 (0.21), residues: 656
  sheet: -0.79 (0.50), residues: 82
  loop : -1.50 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 583 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.016   0.001   PHE A 284 
 TYR   0.014   0.001   TYR A 592 
 ARG   0.001   0.000   ARG A 213 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A  500 MET cc_start: 0.8293 (tmm) cc_final: 0.7693 (tmm)
REVERT: A  628 GLU cc_start: 0.8594 (tp30) cc_final: 0.8262 (tp30)
REVERT: B  500 MET cc_start: 0.8305 (tmm) cc_final: 0.7707 (tmm)
REVERT: B  616 THR cc_start: 0.8208 (t) cc_final: 0.7950 (t)
REVERT: B  628 GLU cc_start: 0.8601 (tp30) cc_final: 0.8283 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1826
  time to fit residues: 34.2790
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0020
   chunk 104 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.9192

-------------------------------------------------------------------------------
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 = 0.3358 r_free = 0.3358 target = 0.099286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.082797 restraints weight = 16423.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.085951 restraints weight = 8178.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.088114 restraints weight = 5044.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8714  Z= 0.176
  Angle     :  0.621  11.023  11778  Z= 0.297
  Chirality :  0.041   0.334   1356
  Planarity :  0.003   0.043   1474
  Dihedral  :  3.833  34.273   1188
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.99 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 1078
  helix:  2.15 (0.21), residues: 656
  sheet: -0.68 (0.50), residues: 82
  loop : -1.48 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 511 
 HIS   0.006   0.001   HIS B 618 
 PHE   0.012   0.001   PHE A 284 
 TYR   0.014   0.001   TYR A 592 
 ARG   0.005   0.000   ARG B 474 

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.057 
Fit side-chains
REVERT: A  500 MET cc_start: 0.8294 (tmm) cc_final: 0.7721 (tmm)
REVERT: A  628 GLU cc_start: 0.8615 (tp30) cc_final: 0.8289 (tp30)
REVERT: B  500 MET cc_start: 0.8316 (tmm) cc_final: 0.7729 (tmm)
REVERT: B  628 GLU cc_start: 0.8598 (tp30) cc_final: 0.8285 (tp30)
  outliers start: 19
  outliers final: 18
  residues processed: 121
  average time/residue: 0.1651
  time to fit residues: 30.0139
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  272 THR
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  455 PHE
Chi-restraints excluded: chain A residue  646 PHE
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  646 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   chunk 89 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0170
   chunk 80 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7018

-------------------------------------------------------------------------------
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 = 0.3350 r_free = 0.3350 target = 0.098397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.081819 restraints weight = 16593.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.084979 restraints weight = 8241.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.087159 restraints weight = 5074.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8714  Z= 0.155
  Angle     :  0.596  10.823  11778  Z= 0.282
  Chirality :  0.041   0.332   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.691  21.082   1188
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.64 %
    Favored  : 78.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.27), residues: 1078
  helix:  2.16 (0.21), residues: 656
  sheet: -0.68 (0.50), residues: 82
  loop : -1.40 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 480 
 HIS   0.005   0.001   HIS B 618 
 PHE   0.012   0.001   PHE A 281 
 TYR   0.012   0.001   TYR B 592 
 ARG   0.004   0.000   ARG B 474 

===============================================================================
Job complete
usr+sys time: 2259.31 seconds
wall clock time: 41 minutes 28.81 seconds (2488.81 seconds total)