Starting phenix.real_space_refine
on Thu Mar  6 05:45:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f0h_28757/03_2025/8f0h_28757.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f0h_28757/03_2025/8f0h_28757.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/8f0h_28757/03_2025/8f0h_28757.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f0h_28757/03_2025/8f0h_28757.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f0h_28757/03_2025/8f0h_28757.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f0h_28757/03_2025/8f0h_28757.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=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3134      2.51       5
     N     839      2.21       5
     O     962      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4959
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 960
      Number of conformers: 2
      Conformer: "B"
        Number of residues, atoms: 123, 959
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 2
      Conformer: "A"
        Number of residues, atoms: 123, 958
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 976
    Chain: "C"
      Number of atoms: 1528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1528
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
    Chain: "D"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 754
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 7, 'TRANS': 92}
    Chain: "H"
      Number of atoms: 887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 887
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "L"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 792
          Classifications: {'peptide': 104}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96}
    Chain: "M"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 6.00, per 1000 atoms: 1.21
  Number of scatterers: 4959
  At special positions: 0
  Unit cell: (67.1, 110, 92.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     962      8.00
     N     839      7.00
     C    3134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG M   1 " - " NAG M   2 "
    BETA1-6
      " NAG M   1 " - " FUC M   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG M   1 " - " ASN C 343 "
  Time building additional restraints: 1.33
  Conformation dependent library (CDL) restraints added in 733.7 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 14 sheets defined
      8.4% alpha, 34.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.73
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.729A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 364 through 371
      removed outlier: 4.453A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 385 through 390
      removed outlier: 3.612A  pdb=" N   ASP C 389 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.232A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'H' and resid 86 through 90
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.678A  pdb=" N   ILE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.543A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 60
      removed outlier: 6.709A  pdb=" N   GLY B  50 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   TYR B  60 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL B  48 " --> pdb=" O   TYR B  60 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA B  33 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B  37 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 60
      removed outlier: 6.709A  pdb=" N   GLY B  50 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   TYR B  60 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL B  48 " --> pdb=" O   TYR B  60 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLY B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   MET B  34 " --> pdb=" O   GLY B  50 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ALA B  33 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   VAL B  37 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR B  94 " --> pdb=" O   THR B 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.669A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS C 432 " --> pdb=" O   LEU C 513 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.382A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA7, first strand: chain 'C' and resid 473 through 474
    Processing sheet with id=AA8, first strand: chain 'D' and resid 18 through 23
    Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 47
      removed outlier: 5.303A  pdb=" N   LEU D  45 " --> pdb=" O   GLN D  36 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   GLN D  36 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASP D  91 " --> pdb=" O   HIS D  96 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   HIS D  96 " --> pdb=" O   ASP D  91 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 11
      removed outlier: 5.956A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11
      removed outlier: 5.956A  pdb=" N   GLY H  10 " --> pdb=" O   THR H 114 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7
      removed outlier: 4.158A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.599A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    168 hydrogen bonds defined for protein.
    405 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: 1.50

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1594
        1.34 -     1.46: 1215
        1.46 -     1.58: 2244
        1.58 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 5084
  Sorted by residual:
  bond pdb=" N   ILE L  75 "
       pdb=" CA  ILE L  75 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.031 1.17e-02 7.31e+03 6.93e+00
  bond pdb=" N   THR L  72 "
       pdb=" CA  THR L  72 "
    ideal  model  delta    sigma   weight residual
    1.455  1.487 -0.032 1.25e-02 6.40e+03 6.53e+00
  bond pdb=" N   PHE L  73 "
       pdb=" CA  PHE L  73 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.21e-02 6.83e+03 5.86e+00
  bond pdb=" N   THR L  74 "
       pdb=" CA  THR L  74 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.19e-02 7.06e+03 5.77e+00
  bond pdb=" N   SER L  77 "
       pdb=" CA  SER L  77 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.28e-02 6.10e+03 5.16e+00
  ... (remaining 5079 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.07: 6641
        1.07 -     2.14: 196
        2.14 -     3.21: 54
        3.21 -     4.28: 12
        4.28 -     5.35: 5
  Bond angle restraints: 6908
  Sorted by residual:
  angle pdb=" N   PHE C 338 "
        pdb=" CA  PHE C 338 "
        pdb=" C   PHE C 338 "
      ideal   model   delta    sigma   weight residual
     114.56  109.83    4.73 1.27e+00 6.20e-01 1.39e+01
  angle pdb=" C   ASN L  76 "
        pdb=" CA  ASN L  76 "
        pdb=" CB  ASN L  76 "
      ideal   model   delta    sigma   weight residual
     117.23  112.26    4.97 1.36e+00 5.41e-01 1.34e+01
  angle pdb=" N   ILE L  75 "
        pdb=" CA  ILE L  75 "
        pdb=" C   ILE L  75 "
      ideal   model   delta    sigma   weight residual
     113.07  108.17    4.90 1.36e+00 5.41e-01 1.30e+01
  angle pdb=" CA  LEU L  78 "
        pdb=" C   LEU L  78 "
        pdb=" O   LEU L  78 "
      ideal   model   delta    sigma   weight residual
     122.37  118.24    4.13 1.15e+00 7.56e-01 1.29e+01
  angle pdb=" N   VAL B  64 "
        pdb=" CA  VAL B  64 "
        pdb=" C   VAL B  64 "
      ideal   model   delta    sigma   weight residual
     106.21  109.83   -3.62 1.07e+00 8.73e-01 1.15e+01
  ... (remaining 6903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.94: 2936
       23.94 -    47.88: 66
       47.88 -    71.83: 6
       71.83 -    95.77: 6
       95.77 -   119.71: 1
  Dihedral angle restraints: 3015
    sinusoidal: 1205
      harmonic: 1810
  Sorted by residual:
  dihedral pdb=" CA  ILE L  29 "
           pdb=" C   ILE L  29 "
           pdb=" N   ASN L  30 "
           pdb=" CA  ASN L  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.89  -24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" C2  FUC M   3 "
           pdb=" C1  FUC M   3 "
           pdb=" O5  FUC M   3 "
           pdb=" C5  FUC M   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.68  -62.03  119.71     1      3.00e+01 1.11e-03 1.60e+01
  dihedral pdb=" C1  FUC M   3 "
           pdb=" C5  FUC M   3 "
           pdb=" O5  FUC M   3 "
           pdb=" C4  FUC M   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.12  -34.07   93.19     1      3.00e+01 1.11e-03 1.13e+01
  ... (remaining 3012 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 575
       0.042 -    0.085: 109
       0.085 -    0.127: 54
       0.127 -    0.169: 2
       0.169 -    0.212: 1
  Chirality restraints: 741
  Sorted by residual:
  chirality pdb=" CA  ILE L  75 "
            pdb=" N   ILE L  75 "
            pdb=" C   ILE L  75 "
            pdb=" CB  ILE L  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" C1  NAG M   2 "
            pdb=" O4  NAG M   1 "
            pdb=" C2  NAG M   2 "
            pdb=" O5  NAG M   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.38   -0.02 2.00e-02 2.50e+03 9.14e-01
  chirality pdb=" CA  LEU L  78 "
            pdb=" N   LEU L  78 "
            pdb=" C   LEU L  78 "
            pdb=" CB  LEU L  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.65   -0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 738 not shown)

  Planarity restraints: 893
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  95 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO L  96 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO L  96 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO L  96 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "   -0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO C 521 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY H 100 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO H 101 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO H 101 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 101 "    0.017 5.00e-02 4.00e+02
  ... (remaining 890 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1089
        2.78 -     3.31: 4566
        3.31 -     3.84: 8336
        3.84 -     4.37: 10055
        4.37 -     4.90: 17201
  Nonbonded interactions: 41247
  Sorted by model distance:
  nonbonded pdb=" O   ASN C 439 "
            pdb=" OG  SER C 443 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OH  TYR L  36 "
            pdb=" OE1 GLN L  89 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OD1 ASP C 364 "
            pdb=" OG  SER C 366 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OG  SER C 469 "
            pdb=" OE1 GLU C 471 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" O   PHE B  29 "
            pdb=" NH2 ARG B  72 "
     model   vdw
     2.378 3.120
  ... (remaining 41242 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             186.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.870
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  211.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
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      :  0.003   0.035   5084  Z= 0.162
  Angle     :  0.500   5.351   6908  Z= 0.300
  Chirality :  0.040   0.212    741
  Planarity :  0.004   0.044    892
  Dihedral  : 10.682 119.710   1851
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  4.71 %
    Favored  : 94.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.33), residues: 624
  helix: -1.83 (1.16), residues: 21
  sheet:  0.74 (0.40), residues: 176
  loop : -0.84 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 107 
 HIS   0.001   0.001   HIS D  96 
 PHE   0.006   0.001   PHE H  67 
 TYR   0.018   0.001   TYR L  91 
 ARG   0.002   0.000   ARG C 509 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 180
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8246 (tp40) cc_final: 0.7954 (mm-40)
REVERT: C  385 THR cc_start: 0.8740 (t) cc_final: 0.8465 (p)
REVERT: D   77 VAL cc_start: 0.6240 (t) cc_final: 0.5985 (p)
REVERT: H   59 TYR cc_start: 0.8847 (m-80) cc_final: 0.8626 (m-80)
REVERT: L   82 ASP cc_start: 0.7534 (m-30) cc_final: 0.6658 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 181
  average time/residue: 0.3105
  time to fit residues: 67.2833
Evaluate side-chains
  123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 2.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 26 optimal weight:    0.3980
   chunk 16 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0050
   chunk 25 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 GLN
H 104 HIS
L  30 ASN
L  34 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.103266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.081318 restraints weight = 10009.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 3.15
r_work: 0.3062 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3075
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3075 r_free = 0.3075    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3075
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079   5084  Z= 0.248
  Angle     :  0.661  11.479   6908  Z= 0.349
  Chirality :  0.045   0.164    741
  Planarity :  0.005   0.046    892
  Dihedral  :  8.271 102.918    760
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.94 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.33), residues: 624
  helix: -2.94 (0.78), residues: 27
  sheet:  0.62 (0.39), residues: 174
  loop : -0.81 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.020   0.001   PHE C 429 
 TYR   0.019   0.002   TYR B  80 
 ARG   0.007   0.001   ARG B  16 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8445 (tp40) cc_final: 0.8216 (mm-40)
REVERT: B   95 TYR cc_start: 0.8401 (m-80) cc_final: 0.8052 (m-80)
REVERT: B  118 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8213 (mmmt)
REVERT: C  420 ASP cc_start: 0.8540 (m-30) cc_final: 0.8323 (m-30)
REVERT: C  471 GLU cc_start: 0.8070 (mp0) cc_final: 0.7737 (mp0)
REVERT: D   37 GLN cc_start: 0.7981 (tt0) cc_final: 0.7199 (tt0)
REVERT: D   52 ASP cc_start: 0.7839 (t0) cc_final: 0.7404 (t0)
REVERT: D   73 THR cc_start: 0.8206 (m) cc_final: 0.7863 (p)
REVERT: D   91 ASP cc_start: 0.7525 (t0) cc_final: 0.7275 (t0)
REVERT: H   26 GLU cc_start: 0.7236 (tp30) cc_final: 0.7029 (mt-10)
REVERT: L    2 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8703 (mp)
  outliers start: 11
  outliers final: 5
  residues processed: 149
  average time/residue: 0.2117
  time to fit residues: 38.5093
Evaluate side-chains
  129 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   11 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
D   6 GLN
H 104 HIS
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.099642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.078337 restraints weight = 10252.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 3.03
r_work: 0.3018 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3025 r_free = 0.3025    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   5084  Z= 0.303
  Angle     :  0.666  11.914   6908  Z= 0.348
  Chirality :  0.045   0.155    741
  Planarity :  0.005   0.048    892
  Dihedral  :  7.986  93.654    760
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.88 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.32), residues: 624
  helix: -3.01 (0.75), residues: 27
  sheet:  0.43 (0.38), residues: 183
  loop : -1.03 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  34 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.012   0.001   PHE H  79 
 TYR   0.022   0.002   TYR B  80 
 ARG   0.006   0.001   ARG B  16 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8515 (tp40) cc_final: 0.8291 (mm-40)
REVERT: B   90 ASP cc_start: 0.8639 (m-30) cc_final: 0.8287 (m-30)
REVERT: B   95 TYR cc_start: 0.8324 (m-80) cc_final: 0.8024 (m-80)
REVERT: C  420 ASP cc_start: 0.8638 (m-30) cc_final: 0.8348 (m-30)
REVERT: D    6 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6662 (pp30)
REVERT: D   34 TRP cc_start: 0.8631 (m100) cc_final: 0.8262 (m100)
REVERT: D   73 THR cc_start: 0.8279 (m) cc_final: 0.7983 (p)
REVERT: D   91 ASP cc_start: 0.7613 (t0) cc_final: 0.7216 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 135
  average time/residue: 0.2548
  time to fit residues: 42.5297
Evaluate side-chains
  130 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   68 ASN
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue   11 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0670
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0030
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.4528

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

Flipped N/Q/H residues before XYZ refinement:
** D   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
H 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.100992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.078815 restraints weight = 10251.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 3.16
r_work: 0.3023 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5084  Z= 0.233
  Angle     :  0.655  12.890   6908  Z= 0.336
  Chirality :  0.044   0.155    741
  Planarity :  0.005   0.048    892
  Dihedral  :  7.627  86.655    760
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 15.63 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.07 (0.32), residues: 624
  helix: -3.14 (0.74), residues: 27
  sheet:  0.45 (0.39), residues: 177
  loop : -1.11 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.010   0.001   PHE H  79 
 TYR   0.022   0.001   TYR B  80 
 ARG   0.007   0.001   ARG B  16 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8461 (tp40) cc_final: 0.8244 (mm-40)
REVERT: B   30 ASP cc_start: 0.8819 (p0) cc_final: 0.8403 (p0)
REVERT: B   31 ASP cc_start: 0.8875 (t0) cc_final: 0.8297 (m-30)
REVERT: B   43 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7673 (mmtm)
REVERT: B   76 LYS cc_start: 0.9138 (ptpp) cc_final: 0.8778 (ptpp)
REVERT: B   87 ARG cc_start: 0.7170 (mtm-85) cc_final: 0.6538 (mtm180)
REVERT: B   90 ASP cc_start: 0.8479 (m-30) cc_final: 0.8022 (m-30)
REVERT: B   95 TYR cc_start: 0.8346 (m-80) cc_final: 0.8052 (m-80)
REVERT: C  357 ARG cc_start: 0.9120 (mtp-110) cc_final: 0.8908 (mtp-110)
REVERT: C  386 LYS cc_start: 0.9431 (mmtm) cc_final: 0.9186 (mmtt)
REVERT: C  420 ASP cc_start: 0.8635 (m-30) cc_final: 0.8305 (m-30)
REVERT: C  471 GLU cc_start: 0.7971 (mp0) cc_final: 0.7763 (mp0)
REVERT: D   34 TRP cc_start: 0.8660 (m100) cc_final: 0.8172 (m100)
REVERT: D   52 ASP cc_start: 0.7907 (m-30) cc_final: 0.7625 (m-30)
REVERT: D   91 ASP cc_start: 0.7624 (t0) cc_final: 0.7149 (t0)
REVERT: D   95 ASP cc_start: 0.8428 (m-30) cc_final: 0.8135 (t0)
REVERT: H   13 GLN cc_start: 0.6353 (tp40) cc_final: 0.5888 (mp10)
  outliers start: 22
  outliers final: 10
  residues processed: 142
  average time/residue: 0.2339
  time to fit residues: 40.8851
Evaluate side-chains
  132 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  445 VAL
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0000
   chunk 33 optimal weight:    0.0010
   chunk 40 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 38 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.101558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.079375 restraints weight = 10330.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 3.18
r_work: 0.3031 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3036
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.64   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3036 r_free = 0.3036    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3036
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5084  Z= 0.211
  Angle     :  0.631  11.863   6908  Z= 0.323
  Chirality :  0.044   0.186    741
  Planarity :  0.005   0.049    892
  Dihedral  :  7.004  72.863    760
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.57 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.02 (0.32), residues: 624
  helix: -3.18 (0.72), residues: 27
  sheet:  0.42 (0.38), residues: 184
  loop : -1.06 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  47 
 HIS   0.002   0.001   HIS C 519 
 PHE   0.009   0.001   PHE H  79 
 TYR   0.019   0.001   TYR B  80 
 ARG   0.007   0.001   ARG B  16 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8819 (p0) cc_final: 0.8462 (p0)
REVERT: B   31 ASP cc_start: 0.8877 (t0) cc_final: 0.8287 (m-30)
REVERT: B   58 ILE cc_start: 0.8983 (mt) cc_final: 0.8779 (mt)
REVERT: B   76 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8819 (ptpp)
REVERT: B   87 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.6752 (mtm180)
REVERT: B   90 ASP cc_start: 0.8388 (m-30) cc_final: 0.7879 (m-30)
REVERT: B   95 TYR cc_start: 0.8279 (m-80) cc_final: 0.8021 (m-80)
REVERT: C  357 ARG cc_start: 0.9141 (mtp-110) cc_final: 0.8919 (mtp-110)
REVERT: C  386 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9195 (mmtt)
REVERT: C  420 ASP cc_start: 0.8688 (m-30) cc_final: 0.8342 (m-30)
REVERT: C  471 GLU cc_start: 0.7936 (mp0) cc_final: 0.7668 (mp0)
REVERT: D   34 TRP cc_start: 0.8687 (m100) cc_final: 0.8235 (m100)
REVERT: D   52 ASP cc_start: 0.7969 (m-30) cc_final: 0.7607 (m-30)
REVERT: D   91 ASP cc_start: 0.7645 (t0) cc_final: 0.7130 (t0)
REVERT: D   95 ASP cc_start: 0.8428 (m-30) cc_final: 0.8179 (t0)
REVERT: H   13 GLN cc_start: 0.6607 (tp40) cc_final: 0.6147 (mp10)
REVERT: L   55 GLU cc_start: 0.8991 (tp30) cc_final: 0.8749 (tp30)
REVERT: L   76 ASN cc_start: 0.7815 (t0) cc_final: 0.7594 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 138
  average time/residue: 0.2453
  time to fit residues: 41.8971
Evaluate side-chains
  126 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0470
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H 104 HIS
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.099024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.076875 restraints weight = 10312.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.15
r_work: 0.2995 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5084  Z= 0.282
  Angle     :  0.651  11.441   6908  Z= 0.335
  Chirality :  0.045   0.200    741
  Planarity :  0.005   0.052    892
  Dihedral  :  6.509  56.804    760
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.33 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.32), residues: 624
  helix: -3.24 (0.69), residues: 27
  sheet:  0.31 (0.38), residues: 184
  loop : -0.99 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  79 
 TYR   0.021   0.002   TYR L  91 
 ARG   0.008   0.001   ARG L  18 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.8823 (p0) cc_final: 0.8594 (p0)
REVERT: B   31 ASP cc_start: 0.8889 (t0) cc_final: 0.8378 (m-30)
REVERT: B   76 LYS cc_start: 0.9165 (ptpp) cc_final: 0.8811 (ptpp)
REVERT: B   87 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.6662 (mtm-85)
REVERT: B   89 GLU cc_start: 0.8538 (mp0) cc_final: 0.8190 (pm20)
REVERT: B   90 ASP cc_start: 0.8388 (m-30) cc_final: 0.7778 (m-30)
REVERT: C  357 ARG cc_start: 0.9151 (mtp-110) cc_final: 0.8917 (mtp-110)
REVERT: C  420 ASP cc_start: 0.8720 (m-30) cc_final: 0.8372 (m-30)
REVERT: C  471 GLU cc_start: 0.7889 (mp0) cc_final: 0.7603 (mp0)
REVERT: D   34 TRP cc_start: 0.8756 (m100) cc_final: 0.8262 (m100)
REVERT: D   52 ASP cc_start: 0.8152 (m-30) cc_final: 0.7751 (m-30)
REVERT: D   91 ASP cc_start: 0.7662 (t0) cc_final: 0.7132 (t0)
REVERT: L   55 GLU cc_start: 0.8985 (tp30) cc_final: 0.8736 (tp30)
  outliers start: 15
  outliers final: 14
  residues processed: 128
  average time/residue: 0.2411
  time to fit residues: 37.5882
Evaluate side-chains
  125 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0980
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  39 GLN
D  37 GLN
H   3 GLN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.099007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.076605 restraints weight = 10210.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 3.15
r_work: 0.2986 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2991
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2991 r_free = 0.2991    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2991
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5084  Z= 0.290
  Angle     :  0.665  10.540   6908  Z= 0.343
  Chirality :  0.045   0.177    741
  Planarity :  0.005   0.052    892
  Dihedral  :  6.172  55.880    760
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.20 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.00 (0.32), residues: 624
  helix: -3.25 (0.69), residues: 27
  sheet:  0.29 (0.39), residues: 184
  loop : -0.96 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 HIS   0.004   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  79 
 TYR   0.023   0.002   TYR B  80 
 ARG   0.008   0.001   ARG L  18 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLN cc_start: 0.7319 (mp10) cc_final: 0.7093 (mp10)
REVERT: B   30 ASP cc_start: 0.8824 (p0) cc_final: 0.8620 (p0)
REVERT: B   31 ASP cc_start: 0.8898 (t0) cc_final: 0.8373 (m-30)
REVERT: B   76 LYS cc_start: 0.9171 (ptpp) cc_final: 0.8853 (ptpp)
REVERT: B   87 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.6518 (mtm-85)
REVERT: B   90 ASP cc_start: 0.8363 (m-30) cc_final: 0.7760 (m-30)
REVERT: C  357 ARG cc_start: 0.9149 (mtp-110) cc_final: 0.8897 (mtp-110)
REVERT: C  420 ASP cc_start: 0.8764 (m-30) cc_final: 0.8407 (m-30)
REVERT: C  471 GLU cc_start: 0.7883 (mp0) cc_final: 0.7487 (mp0)
REVERT: C  509 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8433 (mtt180)
REVERT: D   34 TRP cc_start: 0.8775 (m100) cc_final: 0.8289 (m100)
REVERT: D   52 ASP cc_start: 0.8217 (m-30) cc_final: 0.7805 (m-30)
REVERT: D   91 ASP cc_start: 0.7738 (t0) cc_final: 0.7250 (t0)
REVERT: D   95 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8524 (t0)
REVERT: H   13 GLN cc_start: 0.6763 (tp40) cc_final: 0.6176 (mp10)
REVERT: L   76 ASN cc_start: 0.7779 (t0) cc_final: 0.7573 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 135
  average time/residue: 0.2240
  time to fit residues: 37.0794
Evaluate side-chains
  138 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  478 THR
Chi-restraints excluded: chain C residue  509 ARG
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   28 ILE
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   91 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0570
   chunk 52 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.100084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.077702 restraints weight = 10361.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 3.18
r_work: 0.3002 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5084  Z= 0.217
  Angle     :  0.642   9.508   6908  Z= 0.332
  Chirality :  0.045   0.165    741
  Planarity :  0.005   0.054    892
  Dihedral  :  5.514  55.171    760
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.95 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.33), residues: 624
  helix: -3.18 (0.72), residues: 27
  sheet:  0.42 (0.39), residues: 179
  loop : -0.96 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.010   0.001   PHE H  27 
 TYR   0.021   0.001   TYR B  80 
 ARG   0.009   0.001   ARG L  18 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLN cc_start: 0.7284 (mp10) cc_final: 0.6956 (mp10)
REVERT: B   13 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7399 (mm-40)
REVERT: B   30 ASP cc_start: 0.8756 (p0) cc_final: 0.8518 (p0)
REVERT: B   31 ASP cc_start: 0.8894 (t0) cc_final: 0.8346 (m-30)
REVERT: B   76 LYS cc_start: 0.9163 (ptpp) cc_final: 0.8870 (ptpp)
REVERT: B   87 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.6463 (mtm-85)
REVERT: B   90 ASP cc_start: 0.8234 (m-30) cc_final: 0.7513 (m-30)
REVERT: C  357 ARG cc_start: 0.9171 (mtp-110) cc_final: 0.8917 (mtp-110)
REVERT: C  420 ASP cc_start: 0.8751 (m-30) cc_final: 0.8371 (m-30)
REVERT: C  509 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8368 (mtt180)
REVERT: D    3 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6080 (pp20)
REVERT: D   52 ASP cc_start: 0.8138 (m-30) cc_final: 0.7708 (m-30)
REVERT: D   91 ASP cc_start: 0.7669 (t0) cc_final: 0.7173 (t0)
REVERT: D   95 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8549 (t0)
REVERT: H   13 GLN cc_start: 0.6754 (tp40) cc_final: 0.6194 (mp10)
REVERT: H   92 MET cc_start: 0.8846 (tpt) cc_final: 0.8619 (tpp)
REVERT: L   55 GLU cc_start: 0.9003 (tp30) cc_final: 0.8715 (tp30)
  outliers start: 19
  outliers final: 13
  residues processed: 140
  average time/residue: 0.3332
  time to fit residues: 58.1480
Evaluate side-chains
  140 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  391 CYS
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  509 ARG
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 38 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0980
   chunk 11 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H   3 GLN
H 104 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.099334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.076836 restraints weight = 10258.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 3.17
r_work: 0.2990 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.4051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5084  Z= 0.255
  Angle     :  0.648   9.731   6908  Z= 0.337
  Chirality :  0.044   0.172    741
  Planarity :  0.005   0.051    892
  Dihedral  :  5.332  54.588    760
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.83 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.33), residues: 624
  helix: -3.21 (0.71), residues: 27
  sheet:  0.37 (0.39), residues: 179
  loop : -0.98 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  34 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.011   0.001   PHE H  27 
 TYR   0.024   0.002   TYR B  80 
 ARG   0.010   0.001   ARG L  18 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLN cc_start: 0.7242 (mp10) cc_final: 0.6963 (mp10)
REVERT: B   30 ASP cc_start: 0.8770 (p0) cc_final: 0.8537 (p0)
REVERT: B   31 ASP cc_start: 0.8928 (t0) cc_final: 0.8380 (m-30)
REVERT: B   87 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.6503 (mtm-85)
REVERT: B   90 ASP cc_start: 0.8312 (m-30) cc_final: 0.7611 (m-30)
REVERT: C  357 ARG cc_start: 0.9181 (mtp-110) cc_final: 0.8926 (mtp-110)
REVERT: C  420 ASP cc_start: 0.8778 (m-30) cc_final: 0.8395 (m-30)
REVERT: C  509 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8415 (mtt180)
REVERT: D   34 TRP cc_start: 0.8680 (m100) cc_final: 0.8140 (m100)
REVERT: D   52 ASP cc_start: 0.8249 (m-30) cc_final: 0.7803 (m-30)
REVERT: D   91 ASP cc_start: 0.7746 (t0) cc_final: 0.7299 (t0)
REVERT: D   95 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8555 (t0)
REVERT: H    3 GLN cc_start: 0.7519 (tt0) cc_final: 0.7225 (tm-30)
REVERT: H   13 GLN cc_start: 0.6743 (tp40) cc_final: 0.6166 (mp10)
REVERT: H   92 MET cc_start: 0.8887 (tpt) cc_final: 0.8671 (tpp)
REVERT: L   55 GLU cc_start: 0.8971 (tp30) cc_final: 0.8718 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 136
  average time/residue: 0.2796
  time to fit residues: 47.3444
Evaluate side-chains
  140 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  509 ARG
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.1980
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.099541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.077323 restraints weight = 10251.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 3.15
r_work: 0.2999 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5084  Z= 0.238
  Angle     :  0.656   9.597   6908  Z= 0.341
  Chirality :  0.045   0.178    741
  Planarity :  0.005   0.054    892
  Dihedral  :  5.357  55.096    760
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.59 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.33), residues: 624
  helix: -3.19 (0.72), residues: 27
  sheet:  0.33 (0.39), residues: 180
  loop : -0.96 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  47 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.012   0.001   PHE H  27 
 TYR   0.024   0.001   TYR B  80 
 ARG   0.013   0.001   ARG L  18 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 GLN cc_start: 0.7239 (mp10) cc_final: 0.6946 (mp10)
REVERT: B   19 ARG cc_start: 0.8782 (ttt90) cc_final: 0.8461 (ttt90)
REVERT: B   30 ASP cc_start: 0.8767 (p0) cc_final: 0.8536 (p0)
REVERT: B   31 ASP cc_start: 0.8932 (t0) cc_final: 0.8340 (m-30)
REVERT: B   76 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8838 (ptpp)
REVERT: B   87 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.6535 (mtm-85)
REVERT: B   90 ASP cc_start: 0.8431 (m-30) cc_final: 0.7715 (m-30)
REVERT: C  357 ARG cc_start: 0.9183 (mtp-110) cc_final: 0.8925 (mtp-110)
REVERT: C  420 ASP cc_start: 0.8762 (m-30) cc_final: 0.8389 (m-30)
REVERT: C  509 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8425 (mtt180)
REVERT: D   52 ASP cc_start: 0.8227 (m-30) cc_final: 0.7777 (m-30)
REVERT: D   91 ASP cc_start: 0.7751 (t0) cc_final: 0.7304 (t0)
REVERT: D   95 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (t0)
REVERT: H   13 GLN cc_start: 0.6719 (tp40) cc_final: 0.6137 (mp10)
REVERT: H   92 MET cc_start: 0.8860 (tpt) cc_final: 0.8650 (tpp)
REVERT: L   55 GLU cc_start: 0.8966 (tp30) cc_final: 0.8713 (tp30)
REVERT: L   79 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8531 (tp-100)
  outliers start: 16
  outliers final: 13
  residues processed: 137
  average time/residue: 0.2192
  time to fit residues: 37.0615
Evaluate side-chains
  140 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   57 THR
Chi-restraints excluded: chain B residue  121 THR
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  509 ARG
Chi-restraints excluded: chain C residue  525 CYS
Chi-restraints excluded: chain D residue    6 GLN
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue   95 ASP
Chi-restraints excluded: chain D residue   96 HIS
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   68 THR
Chi-restraints excluded: chain H residue   75 LYS
Chi-restraints excluded: chain H residue  103 LEU
Chi-restraints excluded: chain L residue    5 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    0.0870
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0000
   chunk 13 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.4362

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
H   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.100055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.077870 restraints weight = 10368.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 3.16
r_work: 0.3002 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.59   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5084  Z= 0.222
  Angle     :  0.641   9.379   6908  Z= 0.331
  Chirality :  0.044   0.165    741
  Planarity :  0.005   0.058    892
  Dihedral  :  5.339  54.967    760
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.21 %
    Favored  : 77.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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: -1.02 (0.33), residues: 624
  helix: -2.95 (0.73), residues: 27
  sheet:  0.27 (0.39), residues: 180
  loop : -0.98 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  34 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.013   0.001   PHE H  27 
 TYR   0.023   0.001   TYR B  80 
 ARG   0.010   0.001   ARG L  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4226.72 seconds
wall clock time: 76 minutes 21.47 seconds (4581.47 seconds total)