Starting phenix.real_space_refine
on Wed Sep 17 06:44:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyq_60576/09_2025/8zyq_60576.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyq_60576/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyq_60576/09_2025/8zyq_60576.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyq_60576/09_2025/8zyq_60576.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyq_60576/09_2025/8zyq_60576.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyq_60576/09_2025/8zyq_60576.map"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.61, per 1000 atoms: 0.25
  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: 0.57
  Conformation dependent library (CDL) restraints added in 246.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.12
  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: 0.73

  Time building geometry restraints manager: 0.73 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.760
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.650
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.820
-------------------------------------------------------------------------------
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= 0.220
  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 : 7.07
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (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
 ARG   0.008   0.001   ARG B 665 
 TYR   0.018   0.002   TYR B 616 
 PHE   0.018   0.001   PHE D 656 
 TRP   0.014   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 6485)
  covalent geometry    : angle       0.58649 ( 8798)
  hydrogen bonds       : bond        0.13478 (  460)
  hydrogen bonds       : angle       4.03739 ( 1308)

*********************** 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  : 0.191 
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: 0.0933
  time to fit residues: 12.0391
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  : 0.233 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0370
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.192323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.130783 restraints weight = 7736.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 1.83
r_work: 0.3336 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.0761

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= 0.124
  Angle     :  0.508   6.829   8798  Z= 0.267
  Chirality :  0.038   0.153   1032
  Planarity :  0.004   0.040   1033
  Dihedral  :  9.325 130.545    876
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 24.13 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.31), residues: 752
  helix:  1.26 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.27 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 665 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.015   0.001   PHE C 656 
 TRP   0.014   0.001   TRP A 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6485)
  covalent geometry    : angle       0.50776 ( 8798)
  hydrogen bonds       : bond        0.04063 (  460)
  hydrogen bonds       : angle       3.80361 ( 1308)

*********************** 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
  120 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: A  597 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: B  488 ARG cc_start: 0.2126 (OUTLIER) cc_final: 0.1706 (ppt170)
REVERT: B  633 ASN cc_start: 0.9012 (t0) cc_final: 0.8597 (t0)
REVERT: C  528 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8024 (ttt90)
REVERT: D  629 ASN cc_start: 0.7626 (t0) cc_final: 0.7422 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 114
  average time/residue: 0.0848
  time to fit residues: 12.5279
Evaluate side-chains
  109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
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  574 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 16 optimal weight:    5.9990
   chunk 50 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4234 r_free = 0.4234 target = 0.196121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.134625 restraints weight = 7660.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.94
r_work: 0.3366 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.0984

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= 0.130
  Angle     :  0.502   6.890   8798  Z= 0.263
  Chirality :  0.039   0.181   1032
  Planarity :  0.003   0.036   1033
  Dihedral  :  7.708  77.068    874
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.89 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.31), residues: 752
  helix:  1.31 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.20 (0.63), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 541 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.016   0.001   PHE C 656 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6485)
  covalent geometry    : angle       0.50170 ( 8798)
  hydrogen bonds       : bond        0.03988 (  460)
  hydrogen bonds       : angle       3.75730 ( 1308)

*********************** 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
  125 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8084 (tm-30)
REVERT: A  597 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7714 (m-80)
REVERT: B  488 ARG cc_start: 0.2197 (OUTLIER) cc_final: 0.1691 (ppt170)
REVERT: B  633 ASN cc_start: 0.8890 (t0) cc_final: 0.8482 (t0)
REVERT: C  528 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8097 (ttt90)
REVERT: C  655 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.6788 (mt)
REVERT: D  629 ASN cc_start: 0.7430 (t0) cc_final: 0.7196 (t0)
  outliers start: 23
  outliers final: 10
  residues processed: 119
  average time/residue: 0.0904
  time to fit residues: 14.0696
Evaluate side-chains
  109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 75 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4237 r_free = 0.4237 target = 0.196244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.134247 restraints weight = 7722.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.86
r_work: 0.3373 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1198

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= 0.128
  Angle     :  0.512   6.856   8798  Z= 0.264
  Chirality :  0.039   0.198   1032
  Planarity :  0.003   0.034   1033
  Dihedral  :  7.351  72.707    874
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 23.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.32), residues: 752
  helix:  1.36 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop :  0.20 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 541 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.017   0.001   PHE C 656 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6485)
  covalent geometry    : angle       0.51242 ( 8798)
  hydrogen bonds       : bond        0.03850 (  460)
  hydrogen bonds       : angle       3.70138 ( 1308)

*********************** 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
  132 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  575 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: A  576 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: A  597 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7555 (m-80)
REVERT: B  488 ARG cc_start: 0.2385 (OUTLIER) cc_final: 0.1737 (ppt170)
REVERT: B  499 LEU cc_start: 0.7382 (pt) cc_final: 0.7028 (pp)
REVERT: B  633 ASN cc_start: 0.8968 (t0) cc_final: 0.8562 (t0)
REVERT: C  528 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.8138 (ttt90)
REVERT: C  552 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7511 (mm)
REVERT: C  652 TYR cc_start: 0.6091 (t80) cc_final: 0.5204 (t80)
REVERT: D  629 ASN cc_start: 0.7560 (t0) cc_final: 0.7329 (t0)
  outliers start: 30
  outliers final: 15
  residues processed: 123
  average time/residue: 0.0870
  time to fit residues: 13.8621
Evaluate side-chains
  116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  650 LEU
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  552 LEU
Chi-restraints excluded: chain C residue  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  636 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   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
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 = 0.4228 r_free = 0.4228 target = 0.195558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.133695 restraints weight = 7839.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.87
r_work: 0.3363 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.1338

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= 0.136
  Angle     :  0.529   7.744   8798  Z= 0.271
  Chirality :  0.039   0.179   1032
  Planarity :  0.003   0.033   1033
  Dihedral  :  7.377  75.121    874
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.63 (0.32), residues: 752
  helix:  1.32 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.07 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 541 
 TYR   0.018   0.002   TYR B 616 
 PHE   0.010   0.001   PHE B 498 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.003   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6485)
  covalent geometry    : angle       0.52851 ( 8798)
  hydrogen bonds       : bond        0.03836 (  460)
  hydrogen bonds       : angle       3.70916 ( 1308)

*********************** 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
  122 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8050 (tm-30)
REVERT: A  597 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7579 (m-80)
REVERT: B  488 ARG cc_start: 0.2396 (OUTLIER) cc_final: 0.1717 (ppt170)
REVERT: B  499 LEU cc_start: 0.7366 (pt) cc_final: 0.7023 (pp)
REVERT: B  633 ASN cc_start: 0.8994 (t0) cc_final: 0.8583 (t0)
REVERT: C  528 ARG cc_start: 0.8580 (mtp-110) cc_final: 0.8138 (ttt90)
REVERT: C  652 TYR cc_start: 0.6014 (t80) cc_final: 0.5401 (t80)
  outliers start: 24
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0943
  time to fit residues: 13.8267
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  : 0.227 
-------------------------------------------------------------------------------
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 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  555 CYS
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  636 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
Chi-restraints excluded: chain D residue  554 MET
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 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.196067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.134312 restraints weight = 7875.453|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.88
r_work: 0.3373 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6485  Z= 0.126
  Angle     :  0.514   6.949   8798  Z= 0.265
  Chirality :  0.039   0.208   1032
  Planarity :  0.003   0.032   1033
  Dihedral  :  7.344  76.507    874
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 25.34 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.32), residues: 752
  helix:  1.35 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.05 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 665 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.011   0.001   PHE B 656 
 TRP   0.012   0.001   TRP A 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6485)
  covalent geometry    : angle       0.51364 ( 8798)
  hydrogen bonds       : bond        0.03783 (  460)
  hydrogen bonds       : angle       3.66670 ( 1308)

*********************** 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
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7923 (tm-30)
REVERT: A  597 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7516 (m-80)
REVERT: B  488 ARG cc_start: 0.2286 (OUTLIER) cc_final: 0.1621 (ppt170)
REVERT: B  499 LEU cc_start: 0.7351 (pt) cc_final: 0.7002 (pp)
REVERT: B  530 LEU cc_start: 0.8854 (mt) cc_final: 0.8516 (mp)
REVERT: B  633 ASN cc_start: 0.8966 (t0) cc_final: 0.8576 (t0)
REVERT: C  528 ARG cc_start: 0.8582 (mtp-110) cc_final: 0.8115 (ttt90)
REVERT: C  552 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7575 (mm)
REVERT: C  652 TYR cc_start: 0.6078 (t80) cc_final: 0.5306 (t80)
  outliers start: 27
  outliers final: 19
  residues processed: 118
  average time/residue: 0.1033
  time to fit residues: 15.4461
Evaluate side-chains
  118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
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  573 ASN
Chi-restraints excluded: chain A residue  597 TYR
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 C residue  636 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
Chi-restraints excluded: chain D residue  554 MET
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0770
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.7338

-------------------------------------------------------------------------------
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 = 0.4228 r_free = 0.4228 target = 0.195389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.135472 restraints weight = 7723.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3540 rms_B_bonded: 2.14
r_work: 0.3309 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.1559

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= 0.133
  Angle     :  0.531   8.416   8798  Z= 0.271
  Chirality :  0.039   0.178   1032
  Planarity :  0.003   0.031   1033
  Dihedral  :  7.360  77.127    874
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 25.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.32), residues: 752
  helix:  1.33 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop :  0.04 (0.62), residues: 111

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 541 
 TYR   0.018   0.002   TYR B 616 
 PHE   0.012   0.001   PHE C 463 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6485)
  covalent geometry    : angle       0.53058 ( 8798)
  hydrogen bonds       : bond        0.03799 (  460)
  hydrogen bonds       : angle       3.67319 ( 1308)

*********************** 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: 27
    poor density    : 98
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: A  597 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7536 (m-80)
REVERT: B  488 ARG cc_start: 0.2174 (OUTLIER) cc_final: 0.1540 (ppt170)
REVERT: B  499 LEU cc_start: 0.7341 (pt) cc_final: 0.6994 (pp)
REVERT: B  530 LEU cc_start: 0.8850 (mt) cc_final: 0.8512 (mp)
REVERT: B  633 ASN cc_start: 0.8927 (t0) cc_final: 0.8534 (t0)
REVERT: C  528 ARG cc_start: 0.8655 (mtp-110) cc_final: 0.8063 (ttt90)
REVERT: C  552 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7527 (mm)
REVERT: C  652 TYR cc_start: 0.5906 (t80) cc_final: 0.5271 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 116
  average time/residue: 0.0934
  time to fit residues: 13.9774
Evaluate side-chains
  118 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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 B residue  488 ARG
Chi-restraints excluded: chain B residue  500 ILE
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 C residue  606 SER
Chi-restraints excluded: chain C residue  636 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
Chi-restraints excluded: chain D residue  554 MET
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0170
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.4166 r_free = 0.4166 target = 0.190583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.129169 restraints weight = 7758.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.85
r_work: 0.3313 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1605

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= 0.125
  Angle     :  0.531   8.749   8798  Z= 0.273
  Chirality :  0.039   0.212   1032
  Planarity :  0.003   0.030   1033
  Dihedral  :  7.329  77.462    874
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.28 %
    Favored  : 71.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.32), residues: 752
  helix:  1.35 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop :  0.12 (0.63), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 541 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6485)
  covalent geometry    : angle       0.53128 ( 8798)
  hydrogen bonds       : bond        0.03796 (  460)
  hydrogen bonds       : angle       3.64209 ( 1308)

*********************** 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
  126 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: A  597 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7522 (m-80)
REVERT: B  488 ARG cc_start: 0.2143 (OUTLIER) cc_final: 0.1496 (ppt170)
REVERT: B  499 LEU cc_start: 0.7359 (pt) cc_final: 0.7033 (pp)
REVERT: B  530 LEU cc_start: 0.8872 (mt) cc_final: 0.8531 (mp)
REVERT: B  573 ASN cc_start: 0.8928 (t0) cc_final: 0.8581 (t0)
REVERT: B  633 ASN cc_start: 0.9001 (t0) cc_final: 0.8583 (t0)
REVERT: C  528 ARG cc_start: 0.8650 (mtp-110) cc_final: 0.8022 (ttt90)
REVERT: C  552 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7454 (mm)
REVERT: C  652 TYR cc_start: 0.5760 (t80) cc_final: 0.5197 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0967
  time to fit residues: 14.8723
Evaluate side-chains
  119 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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 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  415 LEU
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 C residue  636 SER
Chi-restraints excluded: chain D residue  428 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
Chi-restraints excluded: chain D residue  554 MET
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 42 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 43 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4153 r_free = 0.4153 target = 0.189389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.129434 restraints weight = 7785.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.82
r_work: 0.3307 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.1661

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= 0.131
  Angle     :  0.539   8.202   8798  Z= 0.273
  Chirality :  0.039   0.171   1032
  Planarity :  0.003   0.034   1033
  Dihedral  :  7.347  78.242    874
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.32), residues: 752
  helix:  1.38 (0.21), residues: 639
  sheet:  None (None), residues: 0
  loop : -0.10 (0.62), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 541 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.011   0.001   PHE B 656 
 TRP   0.012   0.001   TRP A 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6485)
  covalent geometry    : angle       0.53923 ( 8798)
  hydrogen bonds       : bond        0.03763 (  460)
  hydrogen bonds       : angle       3.66436 ( 1308)

*********************** 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
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7928 (tm-30)
REVERT: B  488 ARG cc_start: 0.2170 (OUTLIER) cc_final: 0.1509 (ppt170)
REVERT: B  499 LEU cc_start: 0.7329 (pt) cc_final: 0.7010 (pp)
REVERT: B  530 LEU cc_start: 0.8868 (mt) cc_final: 0.8530 (mp)
REVERT: B  573 ASN cc_start: 0.8902 (t0) cc_final: 0.8553 (t0)
REVERT: B  633 ASN cc_start: 0.9005 (t0) cc_final: 0.8587 (t0)
REVERT: C  528 ARG cc_start: 0.8696 (mtp-110) cc_final: 0.8037 (ttt90)
REVERT: C  552 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7423 (mm)
REVERT: C  651 MET cc_start: 0.8297 (tpp) cc_final: 0.7964 (tpp)
REVERT: C  652 TYR cc_start: 0.5768 (t80) cc_final: 0.5122 (t80)
  outliers start: 25
  outliers final: 21
  residues processed: 113
  average time/residue: 0.1023
  time to fit residues: 14.8756
Evaluate side-chains
  117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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 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  415 LEU
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 C residue  636 SER
Chi-restraints excluded: chain D residue  428 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
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 24 optimal weight:    0.3980
   chunk 67 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.189394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.129590 restraints weight = 7742.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.81
r_work: 0.3311 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6485  Z= 0.128
  Angle     :  0.536   8.145   8798  Z= 0.272
  Chirality :  0.039   0.178   1032
  Planarity :  0.003   0.037   1033
  Dihedral  :  7.123  78.156    872
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.32), residues: 752
  helix:  1.40 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.14 (0.62), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 665 
 TYR   0.017   0.002   TYR B 616 
 PHE   0.011   0.001   PHE B 656 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6485)
  covalent geometry    : angle       0.53589 ( 8798)
  hydrogen bonds       : bond        0.03740 (  460)
  hydrogen bonds       : angle       3.64282 ( 1308)

********************** 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
  121 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  576 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: B  488 ARG cc_start: 0.2139 (OUTLIER) cc_final: 0.1479 (ppt170)
REVERT: B  499 LEU cc_start: 0.7319 (pt) cc_final: 0.6994 (pp)
REVERT: B  530 LEU cc_start: 0.8870 (mt) cc_final: 0.8540 (mp)
REVERT: B  573 ASN cc_start: 0.8885 (t0) cc_final: 0.8536 (t0)
REVERT: B  633 ASN cc_start: 0.9002 (t0) cc_final: 0.8587 (t0)
REVERT: C  528 ARG cc_start: 0.8688 (mtp-110) cc_final: 0.8188 (mtt90)
REVERT: C  552 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7443 (mm)
REVERT: C  651 MET cc_start: 0.8335 (tpp) cc_final: 0.8012 (tpp)
REVERT: C  652 TYR cc_start: 0.5758 (t80) cc_final: 0.5132 (t80)
  outliers start: 24
  outliers final: 20
  residues processed: 113
  average time/residue: 0.1030
  time to fit residues: 14.9323
Evaluate side-chains
  117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
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 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  415 LEU
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 C residue  636 SER
Chi-restraints excluded: chain D residue  428 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
Chi-restraints excluded: chain D residue  554 MET
Chi-restraints excluded: chain D residue  647 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0570
   chunk 66 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.190282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.130742 restraints weight = 7694.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.92
r_work: 0.3304 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6485  Z= 0.119
  Angle     :  0.528   9.122   8798  Z= 0.268
  Chirality :  0.038   0.175   1032
  Planarity :  0.003   0.037   1033
  Dihedral  :  7.089  78.043    872
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 25.95 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.32), residues: 752
  helix:  1.42 (0.21), residues: 638
  sheet:  None (None), residues: 0
  loop : -0.10 (0.63), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 665 
 TYR   0.016   0.001   TYR B 616 
 PHE   0.012   0.001   PHE B 656 
 TRP   0.012   0.001   TRP D 568 
 HIS   0.002   0.001   HIS D 562 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6485)
  covalent geometry    : angle       0.52756 ( 8798)
  hydrogen bonds       : bond        0.03633 (  460)
  hydrogen bonds       : angle       3.60270 ( 1308)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2213.71 seconds
wall clock time: 38 minutes 30.34 seconds (2310.34 seconds total)