Starting phenix.real_space_refine
on Wed Mar 12 22:42:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r8c_24315/03_2025/7r8c_24315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8c_24315/03_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_24315/03_2025/7r8c_24315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_2025/7r8c_24315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_2025/7r8c_24315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8c_24315/03_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-5624/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: 5.00, per 1000 atoms: 0.59
  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: 2.05
  Conformation dependent library (CDL) restraints added in 980.1 milliseconds
  

  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: 0.84
  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: 2.31

  Time building geometry restraints manager: 2.44 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: 0.04
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:             0.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.310
  Find NCS groups from input model:        0.140
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.690
-------------------------------------------------------------------------------
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  : 1.387 
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: 0.2049
  time to fit residues: 60.7679
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  : 1.033 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.080714 restraints weight = 16535.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.083796 restraints weight = 8166.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.085950 restraints weight = 5019.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
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   8.699  11778  Z= 0.304
  Chirality :  0.042   0.153   1356
  Planarity :  0.004   0.036   1474
  Dihedral  :  3.682  18.175   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  : 0.955 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.9019 (t80) cc_final: 0.8727 (t80)
REVERT: A  213 ARG cc_start: 0.8797 (mmt90) cc_final: 0.8503 (mmt90)
REVERT: A  454 MET cc_start: 0.8769 (ppp) cc_final: 0.8566 (tmm)
REVERT: A  500 MET cc_start: 0.8195 (tmm) cc_final: 0.7502 (tmm)
REVERT: A  511 TRP cc_start: 0.8087 (m100) cc_final: 0.7689 (t60)
REVERT: A  595 GLU cc_start: 0.8197 (tt0) cc_final: 0.7926 (tt0)
REVERT: A  628 GLU cc_start: 0.8792 (tp30) cc_final: 0.8572 (tp30)
REVERT: B  155 PHE cc_start: 0.9009 (t80) cc_final: 0.8703 (t80)
REVERT: B  178 MET cc_start: 0.9450 (mmm) cc_final: 0.9249 (mmm)
REVERT: B  213 ARG cc_start: 0.8799 (mmt90) cc_final: 0.8506 (mmt90)
REVERT: B  500 MET cc_start: 0.8197 (tmm) cc_final: 0.7514 (tmm)
REVERT: B  511 TRP cc_start: 0.8069 (m100) cc_final: 0.7689 (t60)
REVERT: B  592 TYR cc_start: 0.8802 (m-80) cc_final: 0.8556 (m-80)
REVERT: B  595 GLU cc_start: 0.8166 (tt0) cc_final: 0.7909 (tt0)
REVERT: B  628 GLU cc_start: 0.8813 (tp30) cc_final: 0.8602 (tp30)
  outliers start: 18
  outliers final: 14
  residues processed: 135
  average time/residue: 0.1864
  time to fit residues: 36.2137
Evaluate side-chains
  129 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 35 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.097547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.080964 restraints weight = 16709.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.084112 restraints weight = 8218.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.086311 restraints weight = 5046.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2019

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= 0.144
  Angle     :  0.512   5.997  11778  Z= 0.255
  Chirality :  0.038   0.144   1356
  Planarity :  0.003   0.036   1474
  Dihedral  :  3.575  18.502   1188
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 13.95 %
    Favored  : 83.91 %
  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:  0.48 (0.27), residues: 1078
  helix:  1.69 (0.21), residues: 638
  sheet: -0.95 (0.45), residues: 82
  loop : -1.97 (0.33), 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   0.013   0.001   TYR A 592 
 ARG   0.002   0.000   ARG A 474 

*********************** 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
  149 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  155 PHE cc_start: 0.9023 (t80) cc_final: 0.8702 (t80)
REVERT: A  179 MET cc_start: 0.9078 (mmm) cc_final: 0.8722 (mmm)
REVERT: A  500 MET cc_start: 0.8257 (tmm) cc_final: 0.7548 (tmm)
REVERT: A  595 GLU cc_start: 0.8244 (tt0) cc_final: 0.8039 (tt0)
REVERT: A  628 GLU cc_start: 0.8816 (tp30) cc_final: 0.8448 (tp30)
REVERT: B  155 PHE cc_start: 0.9035 (t80) cc_final: 0.8689 (t80)
REVERT: B  178 MET cc_start: 0.9474 (mmm) cc_final: 0.9244 (mmm)
REVERT: B  179 MET cc_start: 0.9088 (mmm) cc_final: 0.8756 (mmm)
REVERT: B  500 MET cc_start: 0.8265 (tmm) cc_final: 0.7553 (tmm)
REVERT: B  511 TRP cc_start: 0.8126 (m100) cc_final: 0.7581 (t60)
REVERT: B  592 TYR cc_start: 0.8853 (m-80) cc_final: 0.8624 (m-80)
REVERT: B  595 GLU cc_start: 0.8226 (tt0) cc_final: 0.8010 (tt0)
REVERT: B  628 GLU cc_start: 0.8842 (tp30) cc_final: 0.8501 (tp30)
  outliers start: 20
  outliers final: 12
  residues processed: 139
  average time/residue: 0.1773
  time to fit residues: 35.5616
Evaluate side-chains
  128 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  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  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:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   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:    3.9990
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3250 r_free = 0.3250 target = 0.092264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.075096 restraints weight = 16992.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.078148 restraints weight = 8366.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.080259 restraints weight = 5180.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8714  Z= 0.355
  Angle     :  0.626   6.207  11778  Z= 0.314
  Chirality :  0.043   0.162   1356
  Planarity :  0.004   0.041   1474
  Dihedral  :  3.905  21.303   1188
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 15.77 %
    Favored  : 80.47 %
  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:  0.43 (0.26), residues: 1078
  helix:  1.51 (0.21), residues: 656
  sheet: -1.02 (0.49), residues: 82
  loop : -1.86 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 480 
 HIS   0.010   0.002   HIS B 171 
 PHE   0.016   0.002   PHE B 448 
 TYR   0.009   0.001   TYR B 510 
 ARG   0.004   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
  141 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  179 MET cc_start: 0.9011 (mmm) cc_final: 0.8638 (mmm)
REVERT: A  500 MET cc_start: 0.8216 (tmm) cc_final: 0.7515 (tmm)
REVERT: A  628 GLU cc_start: 0.8878 (tp30) cc_final: 0.8410 (tm-30)
REVERT: B  179 MET cc_start: 0.9014 (mmm) cc_final: 0.8671 (mmm)
REVERT: B  500 MET cc_start: 0.8220 (tmm) cc_final: 0.7518 (tmm)
REVERT: B  512 MET cc_start: 0.9135 (ttm) cc_final: 0.8876 (ttt)
REVERT: B  595 GLU cc_start: 0.8232 (tt0) cc_final: 0.8000 (tt0)
REVERT: B  628 GLU cc_start: 0.8892 (tp30) cc_final: 0.8601 (tp30)
  outliers start: 35
  outliers final: 26
  residues processed: 128
  average time/residue: 0.1841
  time to fit residues: 34.4366
Evaluate side-chains
  129 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
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  564 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  645 ILE
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  432 ILE
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  509 VAL
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  645 ILE
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:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 80 optimal weight:    0.1980
   chunk 49 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 101 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9980
   chunk 67 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.096632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.079230 restraints weight = 16385.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.082472 restraints weight = 7998.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.084699 restraints weight = 4903.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8714  Z= 0.149
  Angle     :  0.516   6.779  11778  Z= 0.258
  Chirality :  0.039   0.160   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.708  20.528   1188
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.17 %
    Favored  : 80.04 %
  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:  0.75 (0.27), residues: 1078
  helix:  1.77 (0.21), residues: 656
  sheet: -1.00 (0.49), residues: 82
  loop : -1.70 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 583 
 HIS   0.007   0.001   HIS A 171 
 PHE   0.014   0.001   PHE A 281 
 TYR   0.008   0.001   TYR A 510 
 ARG   0.002   0.000   ARG B 267 

*********************** 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
  144 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8950 (mmm) cc_final: 0.8633 (mmm)
REVERT: A  500 MET cc_start: 0.8265 (tmm) cc_final: 0.7575 (tmm)
REVERT: A  628 GLU cc_start: 0.8755 (tp30) cc_final: 0.8431 (tp30)
REVERT: B  179 MET cc_start: 0.8999 (mmm) cc_final: 0.8702 (mmm)
REVERT: B  500 MET cc_start: 0.8258 (tmm) cc_final: 0.7568 (tmm)
REVERT: B  512 MET cc_start: 0.9053 (ttm) cc_final: 0.8778 (ttt)
REVERT: B  628 GLU cc_start: 0.8759 (tp30) cc_final: 0.8454 (tp30)
  outliers start: 26
  outliers final: 22
  residues processed: 132
  average time/residue: 0.1775
  time to fit residues: 35.9520
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
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  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  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  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  590 VAL
Chi-restraints excluded: chain B residue  617 CYS
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:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0980
   chunk 89 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3329 r_free = 0.3329 target = 0.097660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.080481 restraints weight = 16340.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.083755 restraints weight = 7916.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.086022 restraints weight = 4827.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   8714  Z= 0.152
  Angle     :  0.528   7.063  11778  Z= 0.260
  Chirality :  0.039   0.181   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.596  19.661   1188
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.49 %
    Favored  : 79.72 %
  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:  1.01 (0.27), residues: 1078
  helix:  1.99 (0.21), residues: 654
  sheet: -0.88 (0.50), residues: 82
  loop : -1.59 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 583 
 HIS   0.009   0.001   HIS B 618 
 PHE   0.013   0.001   PHE A 281 
 TYR   0.022   0.001   TYR B 592 
 ARG   0.002   0.000   ARG B 651 

*********************** 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
  145 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8923 (mmm) cc_final: 0.8651 (mmm)
REVERT: A  500 MET cc_start: 0.8269 (tmm) cc_final: 0.7579 (tmm)
REVERT: A  628 GLU cc_start: 0.8712 (tp30) cc_final: 0.8167 (tm-30)
REVERT: B  179 MET cc_start: 0.8964 (mmm) cc_final: 0.8683 (mmm)
REVERT: B  500 MET cc_start: 0.8261 (tmm) cc_final: 0.7582 (tmm)
REVERT: B  628 GLU cc_start: 0.8733 (tp30) cc_final: 0.8431 (tp30)
  outliers start: 26
  outliers final: 24
  residues processed: 132
  average time/residue: 0.2273
  time to fit residues: 45.2287
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  : 1.789 
-------------------------------------------------------------------------------
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  258 LEU
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  590 VAL
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:    0.2980
   chunk 69 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 57 optimal weight:    0.2980
   chunk 92 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3345 r_free = 0.3345 target = 0.098660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.081763 restraints weight = 16460.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.085057 restraints weight = 7928.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.087322 restraints weight = 4793.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   8714  Z= 0.145
  Angle     :  0.544   7.315  11778  Z= 0.267
  Chirality :  0.040   0.185   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.587  19.471   1188
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.03 %
    Favored  : 79.18 %
  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:  1.13 (0.27), residues: 1078
  helix:  2.05 (0.21), residues: 656
  sheet: -0.76 (0.49), residues: 82
  loop : -1.51 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 480 
 HIS   0.012   0.001   HIS B 618 
 PHE   0.013   0.001   PHE B 281 
 TYR   0.019   0.001   TYR B 592 
 ARG   0.002   0.000   ARG A 213 

*********************** 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
  146 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 1.725 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8900 (mmm) cc_final: 0.8640 (mmm)
REVERT: A  500 MET cc_start: 0.8274 (tmm) cc_final: 0.7608 (tmm)
REVERT: A  628 GLU cc_start: 0.8659 (tp30) cc_final: 0.8157 (tm-30)
REVERT: B  179 MET cc_start: 0.8970 (mmm) cc_final: 0.8694 (mmm)
REVERT: B  500 MET cc_start: 0.8280 (tmm) cc_final: 0.7598 (tmm)
REVERT: B  628 GLU cc_start: 0.8695 (tp30) cc_final: 0.8386 (tp30)
  outliers start: 26
  outliers final: 24
  residues processed: 133
  average time/residue: 0.2419
  time to fit residues: 48.5541
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 1.795 
-------------------------------------------------------------------------------
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  258 LEU
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  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  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:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0870
   chunk 55 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    0.3980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.7960

-------------------------------------------------------------------------------
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 = 0.3333 r_free = 0.3333 target = 0.097431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.080810 restraints weight = 16686.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.083979 restraints weight = 8261.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.086192 restraints weight = 5080.666|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8714  Z= 0.162
  Angle     :  0.567  11.517  11778  Z= 0.279
  Chirality :  0.040   0.174   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.719  32.239   1188
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.67 %
    Favored  : 78.43 %
  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:  1.17 (0.27), residues: 1078
  helix:  2.09 (0.21), residues: 656
  sheet: -0.87 (0.49), residues: 82
  loop : -1.49 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 480 
 HIS   0.009   0.001   HIS B 618 
 PHE   0.015   0.001   PHE B 284 
 TYR   0.017   0.001   TYR B 592 
 ARG   0.003   0.000   ARG B 414 

*********************** 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
  145 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8764 (mmm) cc_final: 0.8546 (mmm)
REVERT: A  500 MET cc_start: 0.8274 (tmm) cc_final: 0.7649 (tmm)
REVERT: A  628 GLU cc_start: 0.8596 (tp30) cc_final: 0.8109 (tm-30)
REVERT: B  500 MET cc_start: 0.8271 (tmm) cc_final: 0.7688 (tmm)
REVERT: B  628 GLU cc_start: 0.8627 (tp30) cc_final: 0.8129 (tm-30)
  outliers start: 27
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1682
  time to fit residues: 32.2413
Evaluate side-chains
  132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
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  258 LEU
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  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  646 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 64 optimal weight:    8.9990
   chunk 63 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3334 r_free = 0.3334 target = 0.097475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.080876 restraints weight = 16548.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.084025 restraints weight = 8228.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.086220 restraints weight = 5084.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8714  Z= 0.167
  Angle     :  0.586  10.840  11778  Z= 0.286
  Chirality :  0.040   0.172   1356
  Planarity :  0.003   0.041   1474
  Dihedral  :  3.769  32.927   1188
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.56 %
    Favored  : 78.76 %
  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:  1.22 (0.27), residues: 1078
  helix:  2.13 (0.21), residues: 656
  sheet: -0.89 (0.48), residues: 82
  loop : -1.47 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 511 
 HIS   0.017   0.002   HIS B 618 
 PHE   0.020   0.001   PHE B 501 
 TYR   0.017   0.001   TYR B 592 
 ARG   0.004   0.000   ARG B 474 

*********************** 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
  148 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8776 (mmm) cc_final: 0.8567 (mmm)
REVERT: A  500 MET cc_start: 0.8298 (tmm) cc_final: 0.7697 (tmm)
REVERT: A  628 GLU cc_start: 0.8610 (tp30) cc_final: 0.8106 (tm-30)
REVERT: B  500 MET cc_start: 0.8278 (tmm) cc_final: 0.7727 (tmm)
REVERT: B  628 GLU cc_start: 0.8617 (tp30) cc_final: 0.8303 (tp30)
  outliers start: 25
  outliers final: 23
  residues processed: 132
  average time/residue: 0.1632
  time to fit residues: 32.1955
Evaluate side-chains
  133 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
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  258 LEU
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  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  646 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0070
   chunk 104 optimal weight:    0.7980
   chunk 63 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.1602

-------------------------------------------------------------------------------
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 = 0.3332 r_free = 0.3332 target = 0.097304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.080737 restraints weight = 16450.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.083812 restraints weight = 8207.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.085978 restraints weight = 5089.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2934

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= 0.197
  Angle     :  0.609   9.531  11778  Z= 0.298
  Chirality :  0.041   0.200   1356
  Planarity :  0.003   0.042   1474
  Dihedral  :  3.708  22.090   1188
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  5.19 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.99 %
    Favored  : 78.43 %
  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:  1.20 (0.27), residues: 1078
  helix:  2.12 (0.21), residues: 656
  sheet: -0.83 (0.48), residues: 82
  loop : -1.50 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 511 
 HIS   0.012   0.002   HIS A 618 
 PHE   0.021   0.001   PHE B 501 
 TYR   0.017   0.001   TYR B 592 
 ARG   0.004   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
  140 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.980 
Fit side-chains
REVERT: A  179 MET cc_start: 0.8756 (mmm) cc_final: 0.8533 (mmm)
REVERT: A  500 MET cc_start: 0.8300 (tmm) cc_final: 0.7722 (tmm)
REVERT: A  628 GLU cc_start: 0.8624 (tp30) cc_final: 0.8111 (tm-30)
REVERT: B  179 MET cc_start: 0.8895 (mmm) cc_final: 0.8665 (mmm)
REVERT: B  500 MET cc_start: 0.8289 (tmm) cc_final: 0.7765 (tmm)
REVERT: B  628 GLU cc_start: 0.8634 (tp30) cc_final: 0.8323 (tp30)
  outliers start: 24
  outliers final: 24
  residues processed: 126
  average time/residue: 0.1624
  time to fit residues: 30.5404
Evaluate side-chains
  137 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 113
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
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  258 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 73 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 93 optimal weight:    4.9990
   chunk 46 optimal weight:    0.1980
   chunk 26 optimal weight:    9.9990
   chunk 89 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    2.0388

-------------------------------------------------------------------------------
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 = 0.3301 r_free = 0.3301 target = 0.095589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.079170 restraints weight = 16948.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.082244 restraints weight = 8380.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.084374 restraints weight = 5157.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8714  Z= 0.277
  Angle     :  0.633   8.927  11778  Z= 0.311
  Chirality :  0.042   0.231   1356
  Planarity :  0.004   0.042   1474
  Dihedral  :  3.925  22.513   1188
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.10 %
    Favored  : 78.43 %
  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:  1.14 (0.27), residues: 1078
  helix:  2.05 (0.21), residues: 656
  sheet: -0.79 (0.49), residues: 82
  loop : -1.50 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 511 
 HIS   0.010   0.001   HIS B 618 
 PHE   0.019   0.002   PHE B 501 
 TYR   0.021   0.001   TYR B 592 
 ARG   0.004   0.000   ARG A 474 

===============================================================================
Job complete
usr+sys time: 2437.66 seconds
wall clock time: 45 minutes 27.58 seconds (2727.58 seconds total)