Starting phenix.real_space_refine
on Tue Feb 11 16:53:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyq_60576/02_2025/8zyq_60576.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyq_60576/02_2025/8zyq_60576.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyq_60576/02_2025/8zyq_60576.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyq_60576/02_2025/8zyq_60576.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyq_60576/02_2025/8zyq_60576.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyq_60576/02_2025/8zyq_60576.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     C    4252      2.51       5
     N    1019      2.21       5
     O    1025      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6329
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1309
          Classifications: {'peptide': 166}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 160}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "D"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1662
          Classifications: {'peptide': 210}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 34
          Unusual residues: {'1II': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.49, per 1000 atoms: 0.87
  Number of scatterers: 6329
  At special positions: 0
  Unit cell: (107.9, 110.39, 76.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     F       2      9.00
     O    1025      8.00
     N    1019      7.00
     C    4252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 719.3 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      82.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 409 through 432
      removed outlier: 3.563A  pdb=" N   LEU A 413 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 520 through 531
      removed outlier: 3.572A  pdb=" N   LEU A 524 " --> pdb=" O   ILE A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 538
    Processing helix  chain 'A' and resid 538 through 543
    Processing helix  chain 'A' and resid 545 through 576
    Processing helix  chain 'A' and resid 584 through 593
      removed outlier: 3.519A  pdb=" N   ASN A 588 " --> pdb=" O   GLY A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 623
    Processing helix  chain 'A' and resid 634 through 663
    Processing helix  chain 'B' and resid 409 through 431
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 453 through 471
      removed outlier: 4.066A  pdb=" N   PHE B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 489 through 497
      removed outlier: 3.505A  pdb=" N   LYS B 495 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 506
    Processing helix  chain 'B' and resid 520 through 530
    Processing helix  chain 'B' and resid 531 through 538
      removed outlier: 4.178A  pdb=" N   VAL B 535 " --> pdb=" O   ARG B 531 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS B 538 " --> pdb=" O   ARG B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
      removed outlier: 3.768A  pdb=" N   TYR B 542 " --> pdb=" O   LYS B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 575
    Processing helix  chain 'B' and resid 584 through 593
      removed outlier: 3.531A  pdb=" N   ASN B 588 " --> pdb=" O   GLY B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 623
    Processing helix  chain 'B' and resid 634 through 665
      removed outlier: 3.727A  pdb=" N   ALA B 653 " --> pdb=" O   SER B 649 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 431
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 453 through 470
    Processing helix  chain 'C' and resid 489 through 496
    Processing helix  chain 'C' and resid 497 through 504
    Processing helix  chain 'C' and resid 520 through 530
      removed outlier: 3.898A  pdb=" N   LEU C 524 " --> pdb=" O   ILE C 521 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LYS C 525 " --> pdb=" O   GLY C 522 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 531 through 538
      removed outlier: 3.969A  pdb=" N   VAL C 535 " --> pdb=" O   ARG C 531 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LYS C 538 " --> pdb=" O   ARG C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 543
      removed outlier: 3.647A  pdb=" N   TYR C 542 " --> pdb=" O   LYS C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 545 through 575
      removed outlier: 3.517A  pdb=" N   GLU C 575 " --> pdb=" O   ILE C 571 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 584 through 593
      removed outlier: 3.619A  pdb=" N   ASN C 588 " --> pdb=" O   GLY C 584 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 606 through 623
    Processing helix  chain 'C' and resid 634 through 665
      removed outlier: 3.701A  pdb=" N   GLN C 664 " --> pdb=" O   SER C 660 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ARG C 665 " --> pdb=" O   ALA C 661 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 432
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 453 through 471
      removed outlier: 3.920A  pdb=" N   PHE D 471 " --> pdb=" O   ILE D 467 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 489 through 495
    Processing helix  chain 'D' and resid 497 through 506
    Processing helix  chain 'D' and resid 521 through 525
    Processing helix  chain 'D' and resid 526 through 531
      removed outlier: 3.994A  pdb=" N   LEU D 530 " --> pdb=" O   ALA D 527 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 532 through 537
    Processing helix  chain 'D' and resid 547 through 574
      removed outlier: 3.510A  pdb=" N   MET D 574 " --> pdb=" O   ALA D 570 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 593
    Processing helix  chain 'D' and resid 606 through 623
    Processing helix  chain 'D' and resid 634 through 663

    460 hydrogen bonds defined for protein.
    1308 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: 1.81

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 908
        1.31 -     1.44: 1894
        1.44 -     1.56: 3633
        1.56 -     1.68: 0
        1.68 -     1.81: 50
  Bond restraints: 6485
  Sorted by residual:
  bond pdb=" C34 1II B1101 "
       pdb=" F02 1II B1101 "
    ideal  model  delta    sigma   weight residual
    1.344  1.189  0.155 2.00e-02 2.50e+03 5.98e+01
  bond pdb=" C17 1II B1101 "
       pdb=" C20 1II B1101 "
    ideal  model  delta    sigma   weight residual
    1.517  1.396  0.121 2.00e-02 2.50e+03 3.69e+01
  bond pdb=" C17 1II B1101 "
       pdb=" C21 1II B1101 "
    ideal  model  delta    sigma   weight residual
    1.514  1.402  0.112 2.00e-02 2.50e+03 3.13e+01
  bond pdb=" C14 1II B1101 "
       pdb=" C18 1II B1101 "
    ideal  model  delta    sigma   weight residual
    1.400  1.334  0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" C14 1II B1101 "
       pdb=" C19 1II B1101 "
    ideal  model  delta    sigma   weight residual
    1.383  1.322  0.061 2.00e-02 2.50e+03 9.38e+00
  ... (remaining 6480 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 8673
        2.13 -     4.26: 100
        4.26 -     6.39: 21
        6.39 -     8.53: 3
        8.53 -    10.66: 1
  Bond angle restraints: 8798
  Sorted by residual:
  angle pdb=" C11 1II B1101 "
        pdb=" N04 1II B1101 "
        pdb=" C12 1II B1101 "
      ideal   model   delta    sigma   weight residual
     116.12  105.46   10.66 3.00e+00 1.11e-01 1.26e+01
  angle pdb=" C07 1II B1101 "
        pdb=" N05 1II B1101 "
        pdb=" C14 1II B1101 "
      ideal   model   delta    sigma   weight residual
     125.68  133.71   -8.03 3.00e+00 1.11e-01 7.16e+00
  angle pdb=" C13 1II B1101 "
        pdb=" C15 1II B1101 "
        pdb=" C17 1II B1101 "
      ideal   model   delta    sigma   weight residual
     114.42  106.47    7.95 3.00e+00 1.11e-01 7.03e+00
  angle pdb=" C   PHE D 424 "
        pdb=" N   THR D 425 "
        pdb=" CA  THR D 425 "
      ideal   model   delta    sigma   weight residual
     121.80  115.49    6.31 2.44e+00 1.68e-01 6.68e+00
  angle pdb=" C   ILE D 655 "
        pdb=" N   PHE D 656 "
        pdb=" CA  PHE D 656 "
      ideal   model   delta    sigma   weight residual
     122.06  117.43    4.63 1.86e+00 2.89e-01 6.18e+00
  ... (remaining 8793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.97: 3535
       29.97 -    59.94: 171
       59.94 -    89.91: 8
       89.91 -   119.88: 2
      119.88 -   149.85: 2
  Dihedral angle restraints: 3718
    sinusoidal: 1421
      harmonic: 2297
  Sorted by residual:
  dihedral pdb=" C10 1II B1101 "
           pdb=" C12 1II B1101 "
           pdb=" N04 1II B1101 "
           pdb=" C13 1II B1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      77.41  -72.44  149.85     1      3.00e+01 1.11e-03 1.99e+01
  dihedral pdb=" C11 1II B1101 "
           pdb=" C12 1II B1101 "
           pdb=" N04 1II B1101 "
           pdb=" C13 1II B1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.46  168.34  133.12     1      3.00e+01 1.11e-03 1.80e+01
  dihedral pdb=" CA  PHE D 656 "
           pdb=" C   PHE D 656 "
           pdb=" N   GLY D 657 "
           pdb=" CA  GLY D 657 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.93   21.07     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 3715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 726
       0.036 -    0.073: 241
       0.073 -    0.109: 55
       0.109 -    0.146: 7
       0.146 -    0.182: 3
  Chirality restraints: 1032
  Sorted by residual:
  chirality pdb=" C07 1II B1101 "
            pdb=" C08 1II B1101 "
            pdb=" C09 1II B1101 "
            pdb=" N05 1II B1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.49    0.18 2.00e-01 2.50e+01 8.32e-01
  chirality pdb=" CA  THR D 425 "
            pdb=" N   THR D 425 "
            pdb=" C   THR D 425 "
            pdb=" CB  THR D 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CA  PHE D 656 "
            pdb=" N   PHE D 656 "
            pdb=" C   PHE D 656 "
            pdb=" CB  PHE D 656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.33e-01
  ... (remaining 1029 not shown)

  Planarity restraints: 1033
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 576 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO D 577 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO D 577 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 577 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE D 656 "   -0.007 2.00e-02 2.50e+03   1.43e-02 2.05e+00
        pdb=" C   PHE D 656 "    0.025 2.00e-02 2.50e+03
        pdb=" O   PHE D 656 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY D 657 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 656 "    0.007 2.00e-02 2.50e+03   1.36e-02 1.84e+00
        pdb=" C   PHE C 656 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PHE C 656 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLY C 657 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1030 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1232
        2.77 -     3.30: 6115
        3.30 -     3.83: 10712
        3.83 -     4.37: 11532
        4.37 -     4.90: 20532
  Nonbonded interactions: 50123
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 619 "
            pdb=" OG1 THR B 623 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER D 543 "
            pdb=" OG  SER D 543 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OH  TYR B 493 "
            pdb=" OD2 ASP B 501 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" N   GLN A 664 "
            pdb=" OE1 GLN A 664 "
     model   vdw
     2.284 3.120
  nonbonded pdb=" O   THR A 421 "
            pdb=" OG1 THR A 425 "
     model   vdw
     2.285 3.040
  ... (remaining 50118 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 407 through 665)
  selection = chain 'C'
  selection = chain 'D'
}

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 individual isotropic
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:             3.080
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     17.950
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
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      :  0.005   0.155   6485  Z= 0.281
  Angle     :  0.586  10.656   8798  Z= 0.287
  Chirality :  0.038   0.182   1032
  Planarity :  0.004   0.048   1033
  Dihedral  : 16.950 149.851   2234
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 24.73 %
    Favored  : 74.81 %
  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:  1.48 (0.31), residues: 752
  helix:  1.20 (0.21), residues: 635
  sheet:  None (None), residues: 0
  loop :  0.17 (0.61), residues: 117

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.018   0.001   PHE D 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.008   0.001   ARG B 665 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: B  494 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7427 (m-10)
REVERT: B  633 ASN cc_start: 0.8937 (t0) cc_final: 0.8570 (t0)
REVERT: C  528 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.7950 (ttt90)
REVERT: C  652 TYR cc_start: 0.5799 (t80) cc_final: 0.4415 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 100
  average time/residue: 0.2431
  time to fit residues: 31.8715
Evaluate side-chains
  98 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain B residue  494 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0970
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
D 664 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.196141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.134319 restraints weight = 7695.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.96
r_work: 0.3365 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.0747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6485  Z= 0.189
  Angle     :  0.522   6.885   8798  Z= 0.275
  Chirality :  0.039   0.155   1032
  Planarity :  0.004   0.041   1033
  Dihedral  :  9.334 128.157    876
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 24.13 %
    Favored  : 73.44 %
  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:  1.53 (0.31), residues: 752
  helix:  1.22 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.22 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.015   0.001   PHE C 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.003   0.000   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: A  597 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7730 (m-80)
REVERT: A  650 LEU cc_start: 0.7687 (tp) cc_final: 0.7485 (tp)
REVERT: B  488 ARG cc_start: 0.2084 (OUTLIER) cc_final: 0.1688 (ppt170)
REVERT: B  633 ASN cc_start: 0.8905 (t0) cc_final: 0.8507 (t0)
REVERT: C  528 ARG cc_start: 0.8533 (mtp-110) cc_final: 0.8023 (ttt90)
REVERT: D  629 ASN cc_start: 0.7441 (t0) cc_final: 0.7216 (t0)
  outliers start: 16
  outliers final: 9
  residues processed: 115
  average time/residue: 0.2205
  time to fit residues: 32.8491
Evaluate side-chains
  110 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  469 ILE
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9990
   chunk 60 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
D 664 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.195872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.133829 restraints weight = 7717.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.98
r_work: 0.3364 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6485  Z= 0.191
  Angle     :  0.501   6.887   8798  Z= 0.264
  Chirality :  0.039   0.169   1032
  Planarity :  0.003   0.037   1033
  Dihedral  :  7.748  76.884    874
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.73 %
    Favored  : 71.47 %
  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:  1.62 (0.31), residues: 752
  helix:  1.30 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.18 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.012   0.001   PHE D 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.006   0.000   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: A  597 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7683 (m-80)
REVERT: A  650 LEU cc_start: 0.7699 (tp) cc_final: 0.7471 (tp)
REVERT: B  488 ARG cc_start: 0.2380 (OUTLIER) cc_final: 0.1750 (ppt170)
REVERT: B  633 ASN cc_start: 0.8902 (t0) cc_final: 0.8502 (t0)
REVERT: C  528 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8114 (ttt90)
REVERT: C  655 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6713 (mt)
REVERT: D  629 ASN cc_start: 0.7433 (t0) cc_final: 0.7198 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 120
  average time/residue: 0.2208
  time to fit residues: 34.0835
Evaluate side-chains
  113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  469 ILE
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue  636 SER
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 41 optimal weight:   10.0000
   chunk 52 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    0.4980
   chunk 17 optimal weight:    0.0670
   chunk 51 optimal weight:    0.0020
   overall best weight:    0.4526

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.197546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.136266 restraints weight = 7787.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.96
r_work: 0.3394 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6485  Z= 0.153
  Angle     :  0.483   6.772   8798  Z= 0.250
  Chirality :  0.037   0.180   1032
  Planarity :  0.003   0.034   1033
  Dihedral  :  7.310  71.644    874
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.04 %
    Favored  : 71.02 %
  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:  1.85 (0.32), residues: 752
  helix:  1.46 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop :  0.25 (0.62), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 568 
 HIS   0.002   0.000   HIS D 562 
 PHE   0.012   0.001   PHE C 656 
 TYR   0.015   0.001   TYR B 616 
 ARG   0.006   0.000   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: A  597 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7668 (m-80)
REVERT: B  488 ARG cc_start: 0.2259 (OUTLIER) cc_final: 0.1660 (ppt170)
REVERT: B  499 LEU cc_start: 0.7344 (pt) cc_final: 0.6996 (pp)
REVERT: B  633 ASN cc_start: 0.8868 (t0) cc_final: 0.8446 (t0)
REVERT: C  528 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8095 (ttt90)
REVERT: C  552 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7416 (mm)
REVERT: C  652 TYR cc_start: 0.5960 (t80) cc_final: 0.5241 (t80)
REVERT: C  655 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6691 (mt)
REVERT: D  629 ASN cc_start: 0.7316 (t0) cc_final: 0.7053 (t0)
  outliers start: 26
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2148
  time to fit residues: 34.1967
Evaluate side-chains
  117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  552 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  655 ILE
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 72 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    6.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN
A 578 HIS
D 576 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.195663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.133485 restraints weight = 7714.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 1.87
r_work: 0.3361 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6485  Z= 0.201
  Angle     :  0.527   7.756   8798  Z= 0.271
  Chirality :  0.039   0.183   1032
  Planarity :  0.003   0.032   1033
  Dihedral  :  7.353  74.669    874
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 25.19 %
    Favored  : 71.02 %
  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:  1.70 (0.32), residues: 752
  helix:  1.36 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.11 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.018   0.001   PHE C 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.006   0.000   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8057 (tm-30)
REVERT: A  597 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7570 (m-80)
REVERT: B  488 ARG cc_start: 0.2311 (OUTLIER) cc_final: 0.1634 (ppt170)
REVERT: B  499 LEU cc_start: 0.7379 (pt) cc_final: 0.7048 (pp)
REVERT: B  633 ASN cc_start: 0.8984 (t0) cc_final: 0.8580 (t0)
REVERT: C  528 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8145 (ttt90)
REVERT: C  552 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7449 (mm)
REVERT: C  652 TYR cc_start: 0.5923 (t80) cc_final: 0.5149 (t80)
  outliers start: 25
  outliers final: 16
  residues processed: 115
  average time/residue: 0.2178
  time to fit residues: 32.1988
Evaluate side-chains
  114 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  469 ILE
Chi-restraints excluded: chain C residue  552 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 46 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.195219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.133709 restraints weight = 7706.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 1.83
r_work: 0.3366 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6485  Z= 0.192
  Angle     :  0.526   8.575   8798  Z= 0.269
  Chirality :  0.039   0.194   1032
  Planarity :  0.003   0.032   1033
  Dihedral  :  7.376  76.419    874
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 25.64 %
    Favored  : 70.41 %
  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:  1.68 (0.32), residues: 752
  helix:  1.35 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.06 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.011   0.001   PHE D 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.005   0.000   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8052 (tm-30)
REVERT: A  597 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7577 (m-80)
REVERT: B  488 ARG cc_start: 0.2303 (OUTLIER) cc_final: 0.1625 (ppt170)
REVERT: B  499 LEU cc_start: 0.7403 (pt) cc_final: 0.7059 (pp)
REVERT: B  633 ASN cc_start: 0.8986 (t0) cc_final: 0.8596 (t0)
REVERT: C  528 ARG cc_start: 0.8591 (mtp-110) cc_final: 0.8115 (ttt90)
REVERT: C  552 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7551 (mm)
REVERT: C  652 TYR cc_start: 0.6010 (t80) cc_final: 0.5386 (t80)
  outliers start: 26
  outliers final: 17
  residues processed: 117
  average time/residue: 0.2282
  time to fit residues: 33.7790
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  469 ILE
Chi-restraints excluded: chain C residue  552 LEU
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 46 optimal weight:    0.0030
   chunk 4 optimal weight:    0.0370
   chunk 16 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   chunk 68 optimal weight:    0.1980
   chunk 23 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.3068

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.198118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137732 restraints weight = 7747.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 1.83
r_work: 0.3424 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6485  Z= 0.140
  Angle     :  0.495   6.758   8798  Z= 0.253
  Chirality :  0.038   0.218   1032
  Planarity :  0.003   0.031   1033
  Dihedral  :  7.258  75.749    874
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.95 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.32), residues: 752
  helix:  1.45 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.19 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 568 
 HIS   0.001   0.000   HIS C 492 
 PHE   0.014   0.001   PHE B 656 
 TYR   0.014   0.001   TYR B 616 
 ARG   0.007   0.001   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7791 (tm-30)
REVERT: A  597 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7414 (m-80)
REVERT: B  488 ARG cc_start: 0.2261 (OUTLIER) cc_final: 0.1649 (ppt170)
REVERT: B  499 LEU cc_start: 0.7362 (pt) cc_final: 0.7011 (pp)
REVERT: B  530 LEU cc_start: 0.8846 (mt) cc_final: 0.8502 (mp)
REVERT: B  633 ASN cc_start: 0.8931 (t0) cc_final: 0.8528 (t0)
REVERT: C  528 ARG cc_start: 0.8640 (mtp-110) cc_final: 0.8082 (ttt90)
REVERT: C  552 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7536 (mm)
REVERT: C  652 TYR cc_start: 0.5994 (t80) cc_final: 0.5769 (t80)
  outliers start: 21
  outliers final: 13
  residues processed: 118
  average time/residue: 0.2069
  time to fit residues: 31.5097
Evaluate side-chains
  117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  616 TYR
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  552 LEU
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain D residue  452 LEU
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   chunk 31 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.190517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.128953 restraints weight = 7698.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.95
r_work: 0.3305 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6485  Z= 0.191
  Angle     :  0.540   9.249   8798  Z= 0.277
  Chirality :  0.040   0.185   1032
  Planarity :  0.003   0.032   1033
  Dihedral  :  7.318  77.826    874
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.56 %
    Favored  : 70.71 %
  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:  1.76 (0.32), residues: 752
  helix:  1.41 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.11 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.013   0.001   PHE C 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.007   0.000   ARG B 541 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7653 (tm-30)
REVERT: A  597 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7552 (m-80)
REVERT: B  488 ARG cc_start: 0.2119 (OUTLIER) cc_final: 0.1447 (ppt170)
REVERT: B  499 LEU cc_start: 0.7348 (pt) cc_final: 0.7024 (pp)
REVERT: B  530 LEU cc_start: 0.8868 (mt) cc_final: 0.8531 (mp)
REVERT: B  633 ASN cc_start: 0.9034 (t0) cc_final: 0.8614 (t0)
REVERT: C  528 ARG cc_start: 0.8652 (mtp-110) cc_final: 0.8057 (ttt90)
REVERT: C  652 TYR cc_start: 0.5759 (t80) cc_final: 0.5123 (t80)
REVERT: D  651 MET cc_start: 0.7910 (ttp) cc_final: 0.7699 (ttt)
  outliers start: 18
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2080
  time to fit residues: 30.2837
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 55 optimal weight:    0.6980
   chunk 42 optimal weight:   10.0000
   chunk 17 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.190171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.132811 restraints weight = 7765.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 2.00
r_work: 0.3287 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6485  Z= 0.188
  Angle     :  0.532   8.119   8798  Z= 0.271
  Chirality :  0.039   0.194   1032
  Planarity :  0.003   0.035   1033
  Dihedral  :  7.300  77.669    874
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 26.10 %
    Favored  : 70.56 %
  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:  1.76 (0.32), residues: 752
  helix:  1.41 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.12 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 568 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.011   0.001   PHE B 656 
 TYR   0.017   0.002   TYR B 616 
 ARG   0.007   0.000   ARG B 665 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: A  597 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7546 (m-80)
REVERT: B  488 ARG cc_start: 0.2186 (OUTLIER) cc_final: 0.1527 (ppt170)
REVERT: B  499 LEU cc_start: 0.7334 (pt) cc_final: 0.7011 (pp)
REVERT: B  530 LEU cc_start: 0.8872 (mt) cc_final: 0.8544 (mp)
REVERT: B  633 ASN cc_start: 0.9005 (t0) cc_final: 0.8594 (t0)
REVERT: C  528 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8027 (ttt90)
REVERT: C  552 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7521 (mm)
REVERT: C  651 MET cc_start: 0.8303 (tpp) cc_final: 0.8004 (tpp)
  outliers start: 22
  outliers final: 17
  residues processed: 110
  average time/residue: 0.2120
  time to fit residues: 30.0618
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  573 ASN
Chi-restraints excluded: chain A residue  597 TYR
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  552 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain D residue  526 THR
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 77 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.189978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.128069 restraints weight = 7786.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.89
r_work: 0.3300 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6485  Z= 0.194
  Angle     :  0.536   7.978   8798  Z= 0.273
  Chirality :  0.039   0.190   1032
  Planarity :  0.003   0.038   1033
  Dihedral  :  7.310  78.235    874
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.25 %
    Favored  : 70.71 %
  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:  1.74 (0.32), residues: 752
  helix:  1.39 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.09 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 
 PHE   0.011   0.001   PHE B 656 
 TYR   0.018   0.002   TYR B 616 
 ARG   0.008   0.001   ARG B 665 

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: B  488 ARG cc_start: 0.2177 (OUTLIER) cc_final: 0.1515 (ppt170)
REVERT: B  499 LEU cc_start: 0.7333 (pt) cc_final: 0.7019 (pp)
REVERT: B  530 LEU cc_start: 0.8876 (mt) cc_final: 0.8541 (mp)
REVERT: B  633 ASN cc_start: 0.9029 (t0) cc_final: 0.8608 (t0)
REVERT: C  528 ARG cc_start: 0.8694 (mtp-110) cc_final: 0.8208 (mtt90)
REVERT: C  552 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7485 (mm)
REVERT: C  651 MET cc_start: 0.8284 (tpp) cc_final: 0.7963 (tpp)
  outliers start: 20
  outliers final: 15
  residues processed: 108
  average time/residue: 0.2119
  time to fit residues: 29.2786
Evaluate side-chains
  113 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 VAL
Chi-restraints excluded: chain A residue  418 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain B residue  488 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  555 CYS
Chi-restraints excluded: chain B residue  574 MET
Chi-restraints excluded: chain B residue  663 ILE
Chi-restraints excluded: chain C residue  432 LEU
Chi-restraints excluded: chain C residue  552 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  606 SER
Chi-restraints excluded: chain D residue  526 THR
Chi-restraints excluded: chain D residue  545 TYR
Chi-restraints excluded: chain D residue  549 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4164 r_free = 0.4164 target = 0.190366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.129486 restraints weight = 7893.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 2.06
r_work: 0.3289 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6485  Z= 0.177
  Angle     :  0.529   7.890   8798  Z= 0.269
  Chirality :  0.039   0.184   1032
  Planarity :  0.003   0.037   1033
  Dihedral  :  7.064  78.348    872
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.71 %
    Favored  : 70.56 %
  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:  1.76 (0.32), residues: 752
  helix:  1.44 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.09 (0.63), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 568 
 HIS   0.002   0.001   HIS D 562 
 PHE   0.011   0.001   PHE B 656 
 TYR   0.017   0.002   TYR B 616 
 ARG   0.008   0.001   ARG B 665 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3838.09 seconds
wall clock time: 68 minutes 42.82 seconds (4122.82 seconds total)