Starting phenix.real_space_refine
on Wed Jun  4 19:52:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wk8_32562/06_2025/7wk8_32562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wk8_32562/06_2025/7wk8_32562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wk8_32562/06_2025/7wk8_32562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wk8_32562/06_2025/7wk8_32562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wk8_32562/06_2025/7wk8_32562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wk8_32562/06_2025/7wk8_32562.cif"
  }
  resolution = 3.61
  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=   0.011
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      16      5.16       5
     C    2512      2.51       5
     N     671      2.21       5
     O     783      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3982
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1662
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201}
    Chain: "D"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1656
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 201}
    Chain: "B"
      Number of atoms: 150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 150
          Classifications: {'peptide': 18}
          Link IDs: {'PTRANS': 2, 'TRANS': 15}
    Chain: "A"
      Number of atoms: 514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 514
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 3, 'TRANS': 62}
  Time building chain proxies: 4.14, per 1000 atoms: 1.04
  Number of scatterers: 3982
  At special positions: 0
  Unit cell: (96.184, 95.091, 61.208, 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      16     16.00
     O     783      8.00
     N     671      7.00
     C    2512      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 147 " - pdb=" SG  CYS C 202 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 138 " - pdb=" SG  CYS D 198 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Conformation dependent library (CDL) restraints added in 523.8 milliseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  970

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 12 sheets defined
      3.3% alpha, 43.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'D' and resid 127 through 132
      removed outlier: 4.250A  pdb=" N   SER D 131 " --> pdb=" O   GLU D 127 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLY D 132 " --> pdb=" O   GLN D 128 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 127 through 132'
    Processing helix  chain 'D' and resid 187 through 192
      removed outlier: 3.977A  pdb=" N   ARG D 192 " --> pdb=" O   ASP D 188 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5
      removed outlier: 3.571A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   VAL C  18 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LEU C  83 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   MET C  81 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 12
      removed outlier: 3.570A  pdb=" N   VAL C  12 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   MET C  34 " --> pdb=" O   MET C  50 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   MET C  50 " --> pdb=" O   MET C  34 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   TRP C  36 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG C  40 " --> pdb=" O   GLY C  44 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 9 through 12
      removed outlier: 3.570A  pdb=" N   VAL C  12 " --> pdb=" O   THR C 117 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ARG C  98 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 127 through 131
      removed outlier: 3.775A  pdb=" N   GLY C 146 " --> pdb=" O   LEU C 131 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   TYR C 182 " --> pdb=" O   GLY C 151 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161
    Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7
      removed outlier: 3.584A  pdb=" N   SER D  22 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE D  21 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   CYS D  23 " --> pdb=" O   PHE D  75 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR D  76 " --> pdb=" O   SER D  69 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.580A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 7.565A  pdb=" N   TRP D  39 " --> pdb=" O   LEU D  51 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU D  51 " --> pdb=" O   TRP D  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13
      removed outlier: 6.580A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   HIS D  94 " --> pdb=" O   ALA D 101 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA D 101 " --> pdb=" O   HIS D  94 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31
    Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 122
      removed outlier: 3.741A  pdb=" N   VAL D 137 " --> pdb=" O   PHE D 122 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   TYR D 177 " --> pdb=" O   ASN D 142 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER D 180 " --> pdb=" O   SER D 166 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER D 166 " --> pdb=" O   SER D 180 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 157 through 158
      removed outlier: 3.897A  pdb=" N   TYR D 196 " --> pdb=" O   PHE D 213 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE D 213 " --> pdb=" O   TYR D 196 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 325 through 328
      removed outlier: 3.538A  pdb=" N   GLY A 550 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   ASP A 574 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   ALA A 575 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 566 " --> pdb=" O   ALA A 575 " (cutoff:3.500A)

    128 hydrogen bonds defined for protein.
    315 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: 1.30

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1262
        1.35 -     1.46: 998
        1.46 -     1.58: 1799
        1.58 -     1.70: 0
        1.70 -     1.82: 22
  Bond restraints: 4081
  Sorted by residual:
  bond pdb=" N   LEU C 184 "
       pdb=" CA  LEU C 184 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.27e-02 6.20e+03 8.18e+00
  bond pdb=" N   THR C 183 "
       pdb=" CA  THR C 183 "
    ideal  model  delta    sigma   weight residual
    1.455  1.490 -0.035 1.26e-02 6.30e+03 7.73e+00
  bond pdb=" C   GLU D 109 "
       pdb=" N   ILE D 110 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.32e-02 5.74e+03 6.18e+00
  bond pdb=" N   SER C 119 "
       pdb=" CA  SER C 119 "
    ideal  model  delta    sigma   weight residual
    1.455  1.479 -0.024 1.18e-02 7.18e+03 4.02e+00
  bond pdb=" N   SER C 185 "
       pdb=" CA  SER C 185 "
    ideal  model  delta    sigma   weight residual
    1.464  1.487 -0.024 1.25e-02 6.40e+03 3.57e+00
  ... (remaining 4076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 5406
        2.05 -     4.11: 118
        4.11 -     6.16: 28
        6.16 -     8.21: 2
        8.21 -    10.27: 3
  Bond angle restraints: 5557
  Sorted by residual:
  angle pdb=" C   SER C 179 "
        pdb=" N   ASP C 180 "
        pdb=" CA  ASP C 180 "
      ideal   model   delta    sigma   weight residual
     122.07  127.27   -5.20 1.43e+00 4.89e-01 1.32e+01
  angle pdb=" C   ALA C 137 "
        pdb=" N   GLN C 138 "
        pdb=" CA  GLN C 138 "
      ideal   model   delta    sigma   weight residual
     122.07  127.19   -5.12 1.43e+00 4.89e-01 1.28e+01
  angle pdb=" C   ILE D 154 "
        pdb=" N   ASP D 155 "
        pdb=" CA  ASP D 155 "
      ideal   model   delta    sigma   weight residual
     122.19  127.23   -5.04 1.41e+00 5.03e-01 1.28e+01
  angle pdb=" C   ASP D 174 "
        pdb=" N   SER D 175 "
        pdb=" CA  SER D 175 "
      ideal   model   delta    sigma   weight residual
     122.19  127.16   -4.97 1.41e+00 5.03e-01 1.24e+01
  angle pdb=" C   ASN C 162 "
        pdb=" N   SER C 163 "
        pdb=" CA  SER C 163 "
      ideal   model   delta    sigma   weight residual
     122.34  127.21   -4.87 1.39e+00 5.18e-01 1.23e+01
  ... (remaining 5552 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.81: 2296
       11.81 -    23.62: 110
       23.62 -    35.43: 33
       35.43 -    47.24: 17
       47.24 -    59.05: 1
  Dihedral angle restraints: 2457
    sinusoidal: 955
      harmonic: 1502
  Sorted by residual:
  dihedral pdb=" CA  TRP C 195 "
           pdb=" C   TRP C 195 "
           pdb=" N   PRO C 196 "
           pdb=" CA  PRO C 196 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  dihedral pdb=" CA  TYR C 101 "
           pdb=" C   TYR C 101 "
           pdb=" N   ASP C 102 "
           pdb=" CA  ASP C 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.84   18.16     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  LYS A 535 "
           pdb=" C   LYS A 535 "
           pdb=" N   ASN A 536 "
           pdb=" CA  ASN A 536 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.20  -16.80     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 2454 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 532
       0.066 -    0.132: 79
       0.132 -    0.199: 10
       0.199 -    0.265: 2
       0.265 -    0.331: 2
  Chirality restraints: 625
  Sorted by residual:
  chirality pdb=" CB  ILE D 121 "
            pdb=" CA  ILE D 121 "
            pdb=" CG1 ILE D 121 "
            pdb=" CG2 ILE D 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.74e+00
  chirality pdb=" CB  VAL C 188 "
            pdb=" CA  VAL C 188 "
            pdb=" CG1 VAL C 188 "
            pdb=" CG2 VAL C 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.73e+00
  chirality pdb=" CB  VAL C 204 "
            pdb=" CA  VAL C 204 "
            pdb=" CG1 VAL C 204 "
            pdb=" CG2 VAL C 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 622 not shown)

  Planarity restraints: 712
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 118 "    0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   VAL C 118 "   -0.071 2.00e-02 2.50e+03
        pdb=" O   VAL C 118 "    0.027 2.00e-02 2.50e+03
        pdb=" N   SER C 119 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C 195 "    0.047 5.00e-02 4.00e+02   7.01e-02 7.86e+00
        pdb=" N   PRO C 196 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO C 196 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 196 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 204 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.60e+00
        pdb=" C   VAL C 204 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   VAL C 204 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ALA C 205 "    0.014 2.00e-02 2.50e+03
  ... (remaining 709 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 749
        2.79 -     3.32: 3126
        3.32 -     3.84: 6244
        3.84 -     4.37: 6603
        4.37 -     4.90: 11958
  Nonbonded interactions: 28680
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  22 "
            pdb=" OD1 ASP D  74 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OD1 ASN C  61 "
            pdb=" N   GLN C  62 "
     model   vdw
     2.374 3.120
  nonbonded pdb=" O   PRO C   7 "
            pdb=" OG1 THR C 114 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" OG  SER D 205 "
            pdb=" O   SER D 207 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" O   ALA C 105 "
            pdb=" OG  SER D  95 "
     model   vdw
     2.403 3.040
  ... (remaining 28675 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.320
  Find NCS groups from input model:        0.050
  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:3.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
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      :  0.004   0.054   4086  Z= 0.210
  Angle     :  0.743  10.268   5567  Z= 0.419
  Chirality :  0.054   0.331    625
  Planarity :  0.006   0.070    712
  Dihedral  :  8.507  59.046   1472
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.94 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.22 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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: -1.34 (0.31), residues: 508
  helix: -4.97 (0.38), residues: 8
  sheet: -0.12 (0.30), residues: 220
  loop : -1.41 (0.30), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D  39 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.021   0.002   PHE D 143 
 TYR   0.014   0.001   TYR C 103 
 ARG   0.004   0.000   ARG D  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23575 (  121)
  hydrogen bonds       : angle       8.54891 (  315)
  SS BOND              : bond        0.00153 (    5)
  SS BOND              : angle       0.98373 (   10)
  covalent geometry    : bond        0.00404 ( 4081)
  covalent geometry    : angle       0.74282 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.417 
Fit side-chains
REVERT: C   38 LYS cc_start: 0.8215 (tttt) cc_final: 0.8007 (tttt)
REVERT: C   61 ASN cc_start: 0.8783 (t0) cc_final: 0.8576 (t0)
REVERT: C   63 LYS cc_start: 0.8882 (tttt) cc_final: 0.8569 (ttpp)
REVERT: C   88 SER cc_start: 0.8757 (p) cc_final: 0.8480 (p)
REVERT: C   91 SER cc_start: 0.8041 (m) cc_final: 0.7726 (p)
REVERT: C  114 THR cc_start: 0.7706 (m) cc_final: 0.7418 (p)
REVERT: C  144 THR cc_start: 0.8047 (m) cc_final: 0.7792 (m)
REVERT: C  172 THR cc_start: 0.8640 (m) cc_final: 0.8403 (p)
REVERT: C  193 SER cc_start: 0.7975 (p) cc_final: 0.7677 (p)
REVERT: D   37 MET cc_start: 0.7757 (tpp) cc_final: 0.6524 (tpp)
REVERT: D   86 ASP cc_start: 0.8105 (m-30) cc_final: 0.7819 (m-30)
REVERT: D  215 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8179 (ttp80)
  outliers start: 1
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1746
  time to fit residues: 20.3346
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 28 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
C 178 GLN
D   6 GLN
D  42 GLN
B 331 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.095575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.084144 restraints weight = 7158.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.086187 restraints weight = 4131.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.087534 restraints weight = 2807.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   4086  Z= 0.228
  Angle     :  0.622   5.024   5567  Z= 0.325
  Chirality :  0.045   0.151    625
  Planarity :  0.005   0.044    712
  Dihedral  :  4.513  23.429    551
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.97 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  :  5.54 %
    Favored  : 92.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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: -0.56 (0.34), residues: 508
  helix: -2.93 (1.45), residues: 7
  sheet:  0.33 (0.32), residues: 221
  loop : -0.88 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  39 
 HIS   0.008   0.003   HIS D 193 
 PHE   0.017   0.002   PHE C 153 
 TYR   0.013   0.002   TYR D  53 
 ARG   0.006   0.001   ARG A 567 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  121)
  hydrogen bonds       : angle       6.75456 (  315)
  SS BOND              : bond        0.00539 (    5)
  SS BOND              : angle       1.06732 (   10)
  covalent geometry    : bond        0.00525 ( 4081)
  covalent geometry    : angle       0.62101 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.454 
Fit side-chains
REVERT: C   63 LYS cc_start: 0.8810 (tttt) cc_final: 0.8599 (ttpp)
REVERT: C   91 SER cc_start: 0.8466 (m) cc_final: 0.8013 (p)
REVERT: C  115 LEU cc_start: 0.8265 (tp) cc_final: 0.7982 (tt)
REVERT: C  193 SER cc_start: 0.8222 (p) cc_final: 0.8014 (p)
REVERT: C  204 VAL cc_start: 0.8088 (p) cc_final: 0.7732 (m)
REVERT: C  215 LYS cc_start: 0.7352 (mmmt) cc_final: 0.6495 (mmmt)
REVERT: D   29 VAL cc_start: 0.8398 (m) cc_final: 0.8072 (p)
REVERT: D   37 MET cc_start: 0.7725 (tpp) cc_final: 0.7354 (mmm)
REVERT: D   86 ASP cc_start: 0.8289 (m-30) cc_final: 0.7982 (m-30)
REVERT: D  215 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8260 (ttp80)
  outliers start: 7
  outliers final: 5
  residues processed: 99
  average time/residue: 0.1537
  time to fit residues: 19.0054
Evaluate side-chains
  96 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain A residue  569 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 44 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0170
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
C   1 GLN
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
D   6 GLN
A 532 ASN
A 580 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.093289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.081878 restraints weight = 7114.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.083843 restraints weight = 4138.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.085138 restraints weight = 2839.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   4086  Z= 0.203
  Angle     :  0.590   5.999   5567  Z= 0.303
  Chirality :  0.044   0.136    625
  Planarity :  0.004   0.035    712
  Dihedral  :  4.459  24.980    551
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.36 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  7.76 %
    Favored  : 89.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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: -0.26 (0.34), residues: 508
  helix: -2.60 (1.62), residues: 8
  sheet:  0.71 (0.34), residues: 209
  loop : -0.78 (0.33), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  39 
 HIS   0.005   0.002   HIS D  80 
 PHE   0.011   0.002   PHE C 153 
 TYR   0.013   0.002   TYR C  80 
 ARG   0.003   0.000   ARG B 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  121)
  hydrogen bonds       : angle       6.69291 (  315)
  SS BOND              : bond        0.00363 (    5)
  SS BOND              : angle       0.77047 (   10)
  covalent geometry    : bond        0.00468 ( 4081)
  covalent geometry    : angle       0.58945 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.463 
Fit side-chains
REVERT: C   63 LYS cc_start: 0.8837 (tttt) cc_final: 0.8555 (ttpp)
REVERT: C   91 SER cc_start: 0.8561 (m) cc_final: 0.8101 (p)
REVERT: C  193 SER cc_start: 0.8231 (p) cc_final: 0.8027 (p)
REVERT: C  204 VAL cc_start: 0.8277 (p) cc_final: 0.7955 (m)
REVERT: C  215 LYS cc_start: 0.7300 (mmmt) cc_final: 0.6399 (mmmt)
REVERT: D   37 MET cc_start: 0.7738 (tpp) cc_final: 0.7374 (mmm)
REVERT: D   86 ASP cc_start: 0.8276 (m-30) cc_final: 0.7928 (m-30)
REVERT: D  215 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8339 (ttp80)
  outliers start: 11
  outliers final: 9
  residues processed: 85
  average time/residue: 0.1742
  time to fit residues: 18.6650
Evaluate side-chains
  84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue  149 VAL
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  150 VAL
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  210 VAL
Chi-restraints excluded: chain A residue  571 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0980
   chunk 4 optimal weight:    0.6980
   chunk 42 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0870
   chunk 2 optimal weight:    0.0770
   overall best weight:    0.2916

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.092469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.081313 restraints weight = 7184.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.083345 restraints weight = 4142.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.084692 restraints weight = 2786.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   4086  Z= 0.149
  Angle     :  0.540   5.319   5567  Z= 0.276
  Chirality :  0.043   0.133    625
  Planarity :  0.004   0.032    712
  Dihedral  :  4.213  23.545    551
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.76 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.42 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.01 (0.36), residues: 508
  helix: -2.12 (1.84), residues: 8
  sheet:  0.86 (0.34), residues: 211
  loop : -0.58 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D  39 
 HIS   0.003   0.001   HIS D 202 
 PHE   0.008   0.001   PHE C 153 
 TYR   0.009   0.001   TYR C  80 
 ARG   0.003   0.000   ARG D 159 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03346 (  121)
  hydrogen bonds       : angle       6.40899 (  315)
  SS BOND              : bond        0.00318 (    5)
  SS BOND              : angle       0.67959 (   10)
  covalent geometry    : bond        0.00344 ( 4081)
  covalent geometry    : angle       0.53953 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.433 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8596 (m) cc_final: 0.8135 (p)
REVERT: C  193 SER cc_start: 0.8292 (p) cc_final: 0.8076 (p)
REVERT: C  204 VAL cc_start: 0.8291 (p) cc_final: 0.8000 (m)
REVERT: C  215 LYS cc_start: 0.7390 (mmmt) cc_final: 0.6501 (mmmt)
REVERT: D    1 ASP cc_start: 0.8430 (p0) cc_final: 0.8098 (p0)
REVERT: D   37 MET cc_start: 0.7688 (tpp) cc_final: 0.7133 (tmm)
REVERT: D   86 ASP cc_start: 0.8303 (m-30) cc_final: 0.7949 (m-30)
REVERT: D  152 TRP cc_start: 0.8820 (m100) cc_final: 0.8153 (m100)
REVERT: D  215 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8340 (ttp80)
  outliers start: 8
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1667
  time to fit residues: 16.1251
Evaluate side-chains
  82 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.0770
   chunk 1 optimal weight:    0.0370
   chunk 0 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 11 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   chunk 25 optimal weight:    0.0020
   overall best weight:    0.1424

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
D   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.093508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.082261 restraints weight = 7377.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.084290 restraints weight = 4241.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.085617 restraints weight = 2863.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4086  Z= 0.097
  Angle     :  0.499   6.284   5567  Z= 0.252
  Chirality :  0.042   0.131    625
  Planarity :  0.003   0.034    712
  Dihedral  :  4.014  24.953    551
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.56 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 10.86 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.20 (0.37), residues: 508
  helix: -1.55 (1.97), residues: 8
  sheet:  0.90 (0.34), residues: 220
  loop : -0.43 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D  39 
 HIS   0.002   0.001   HIS D 193 
 PHE   0.006   0.001   PHE C  29 
 TYR   0.007   0.001   TYR D  53 
 ARG   0.002   0.000   ARG A 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02838 (  121)
  hydrogen bonds       : angle       6.06737 (  315)
  SS BOND              : bond        0.00293 (    5)
  SS BOND              : angle       0.64589 (   10)
  covalent geometry    : bond        0.00220 ( 4081)
  covalent geometry    : angle       0.49900 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.748 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8671 (m) cc_final: 0.8227 (p)
REVERT: C  193 SER cc_start: 0.8271 (p) cc_final: 0.8064 (p)
REVERT: C  204 VAL cc_start: 0.8228 (p) cc_final: 0.7957 (m)
REVERT: C  215 LYS cc_start: 0.7352 (mmmt) cc_final: 0.6452 (mmmt)
REVERT: D    1 ASP cc_start: 0.8437 (p0) cc_final: 0.8105 (p0)
REVERT: D   37 MET cc_start: 0.7645 (tpp) cc_final: 0.7106 (tmm)
REVERT: D   86 ASP cc_start: 0.8328 (m-30) cc_final: 0.7968 (m-30)
REVERT: D  152 TRP cc_start: 0.8800 (m100) cc_final: 0.8206 (m100)
REVERT: D  215 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8319 (ttp80)
REVERT: A  584 ILE cc_start: 0.8362 (mm) cc_final: 0.8152 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 79
  average time/residue: 0.1800
  time to fit residues: 17.9498
Evaluate side-chains
  81 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 19 optimal weight:    0.1980
   chunk 42 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0570
   chunk 26 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0770
   chunk 39 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
D   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.091396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.080148 restraints weight = 7263.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.082153 restraints weight = 4167.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.083486 restraints weight = 2807.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4086  Z= 0.154
  Angle     :  0.537   6.224   5567  Z= 0.272
  Chirality :  0.042   0.138    625
  Planarity :  0.004   0.031    712
  Dihedral  :  4.142  23.374    551
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.74 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.53 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.27 (0.36), residues: 508
  helix: -1.29 (2.10), residues: 8
  sheet:  0.99 (0.34), residues: 221
  loop : -0.44 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  39 
 HIS   0.003   0.001   HIS D 202 
 PHE   0.008   0.001   PHE C 153 
 TYR   0.009   0.001   TYR D  91 
 ARG   0.002   0.000   ARG A 577 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  121)
  hydrogen bonds       : angle       6.30837 (  315)
  SS BOND              : bond        0.00336 (    5)
  SS BOND              : angle       0.70146 (   10)
  covalent geometry    : bond        0.00355 ( 4081)
  covalent geometry    : angle       0.53652 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.490 
Fit side-chains
REVERT: C   39 GLN cc_start: 0.7429 (tt0) cc_final: 0.7140 (mt0)
REVERT: C   91 SER cc_start: 0.8693 (m) cc_final: 0.8255 (p)
REVERT: C  204 VAL cc_start: 0.8289 (p) cc_final: 0.8028 (m)
REVERT: C  215 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6573 (mmmt)
REVERT: D    1 ASP cc_start: 0.8432 (p0) cc_final: 0.8117 (p0)
REVERT: D   32 SER cc_start: 0.8671 (m) cc_final: 0.8309 (p)
REVERT: D   37 MET cc_start: 0.7659 (tpp) cc_final: 0.7148 (tmm)
REVERT: D   86 ASP cc_start: 0.8349 (m-30) cc_final: 0.7981 (m-30)
REVERT: D  152 TRP cc_start: 0.8828 (m100) cc_final: 0.8167 (m100)
REVERT: D  215 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8306 (ttp80)
REVERT: A  584 ILE cc_start: 0.8355 (mm) cc_final: 0.8147 (mm)
  outliers start: 10
  outliers final: 10
  residues processed: 77
  average time/residue: 0.1694
  time to fit residues: 16.3940
Evaluate side-chains
  79 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
D   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.089940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.078691 restraints weight = 7400.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.080733 restraints weight = 4203.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.082096 restraints weight = 2800.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4086  Z= 0.193
  Angle     :  0.577   6.729   5567  Z= 0.296
  Chirality :  0.043   0.141    625
  Planarity :  0.004   0.031    712
  Dihedral  :  4.360  22.780    551
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.54 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 10.42 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.19 (0.36), residues: 508
  helix: -1.33 (2.06), residues: 8
  sheet:  1.06 (0.34), residues: 220
  loop : -0.61 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  39 
 HIS   0.005   0.001   HIS D  80 
 PHE   0.010   0.002   PHE C 153 
 TYR   0.011   0.001   TYR C  80 
 ARG   0.002   0.000   ARG D 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (  121)
  hydrogen bonds       : angle       6.64122 (  315)
  SS BOND              : bond        0.00370 (    5)
  SS BOND              : angle       0.74848 (   10)
  covalent geometry    : bond        0.00446 ( 4081)
  covalent geometry    : angle       0.57693 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.430 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8705 (m) cc_final: 0.8235 (p)
REVERT: C  204 VAL cc_start: 0.8368 (p) cc_final: 0.8093 (m)
REVERT: C  215 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6545 (mmmt)
REVERT: D    1 ASP cc_start: 0.8461 (p0) cc_final: 0.8144 (p0)
REVERT: D   32 SER cc_start: 0.8808 (m) cc_final: 0.8450 (p)
REVERT: D   37 MET cc_start: 0.7609 (tpp) cc_final: 0.7346 (mmm)
REVERT: D   86 ASP cc_start: 0.8359 (m-30) cc_final: 0.8006 (m-30)
REVERT: D  152 TRP cc_start: 0.8837 (m100) cc_final: 0.8097 (m100)
REVERT: D  213 PHE cc_start: 0.8797 (p90) cc_final: 0.8479 (p90)
REVERT: D  215 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8295 (ttp80)
  outliers start: 14
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1537
  time to fit residues: 16.0585
Evaluate side-chains
  83 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue  148 ILE
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0970
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
D   6 GLN
A 532 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.089438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.078444 restraints weight = 7281.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.080416 restraints weight = 4132.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.081760 restraints weight = 2771.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   4086  Z= 0.204
  Angle     :  0.584   7.008   5567  Z= 0.299
  Chirality :  0.043   0.142    625
  Planarity :  0.004   0.045    712
  Dihedral  :  4.413  22.340    551
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.54 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 10.86 %
    Favored  : 86.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.16 (0.36), residues: 508
  helix: -1.34 (2.06), residues: 8
  sheet:  1.07 (0.34), residues: 221
  loop : -0.66 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  39 
 HIS   0.005   0.001   HIS D  80 
 PHE   0.011   0.002   PHE C 153 
 TYR   0.010   0.002   TYR C  80 
 ARG   0.002   0.000   ARG D 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  121)
  hydrogen bonds       : angle       6.68703 (  315)
  SS BOND              : bond        0.00404 (    5)
  SS BOND              : angle       1.31465 (   10)
  covalent geometry    : bond        0.00470 ( 4081)
  covalent geometry    : angle       0.58166 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.419 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8702 (m) cc_final: 0.8228 (p)
REVERT: C  204 VAL cc_start: 0.8403 (p) cc_final: 0.8050 (m)
REVERT: C  215 LYS cc_start: 0.7439 (mmmt) cc_final: 0.6609 (mmmt)
REVERT: D    1 ASP cc_start: 0.8482 (p0) cc_final: 0.8160 (p0)
REVERT: D   32 SER cc_start: 0.8815 (m) cc_final: 0.8462 (p)
REVERT: D   58 LEU cc_start: 0.7856 (tp) cc_final: 0.7543 (tt)
REVERT: D   77 LEU cc_start: 0.4104 (mt) cc_final: 0.3759 (tp)
REVERT: D   86 ASP cc_start: 0.8366 (m-30) cc_final: 0.8029 (m-30)
REVERT: D  140 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7532 (mt)
REVERT: D  152 TRP cc_start: 0.8833 (m100) cc_final: 0.8170 (m100)
REVERT: D  215 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8310 (ttp80)
  outliers start: 12
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1659
  time to fit residues: 18.9280
Evaluate side-chains
  93 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  571 ASP
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 46 optimal weight:    0.1980
   chunk 47 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0980
   chunk 23 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0050
   overall best weight:    0.1592

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

Flipped N/Q/H residues before XYZ refinement:
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
A 532 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.091181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.080104 restraints weight = 7350.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.082123 restraints weight = 4175.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.083453 restraints weight = 2790.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4086  Z= 0.111
  Angle     :  0.544   7.088   5567  Z= 0.268
  Chirality :  0.043   0.136    625
  Planarity :  0.004   0.040    712
  Dihedral  :  4.170  24.614    551
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.95 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 11.97 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.34 (0.37), residues: 508
  helix: -0.93 (2.23), residues: 8
  sheet:  1.17 (0.34), residues: 220
  loop : -0.52 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  39 
 HIS   0.002   0.001   HIS D 202 
 PHE   0.006   0.001   PHE C  29 
 TYR   0.007   0.001   TYR D  53 
 ARG   0.001   0.000   ARG B 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02952 (  121)
  hydrogen bonds       : angle       6.34459 (  315)
  SS BOND              : bond        0.00399 (    5)
  SS BOND              : angle       1.00563 (   10)
  covalent geometry    : bond        0.00259 ( 4081)
  covalent geometry    : angle       0.54313 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.430 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8672 (m) cc_final: 0.8222 (p)
REVERT: C  204 VAL cc_start: 0.8338 (p) cc_final: 0.8061 (m)
REVERT: C  215 LYS cc_start: 0.7340 (mmmt) cc_final: 0.6558 (mmmt)
REVERT: D    1 ASP cc_start: 0.8458 (p0) cc_final: 0.8131 (p0)
REVERT: D   32 SER cc_start: 0.8758 (m) cc_final: 0.8390 (p)
REVERT: D   37 MET cc_start: 0.7559 (mmm) cc_final: 0.7152 (tmm)
REVERT: D   58 LEU cc_start: 0.7808 (tp) cc_final: 0.7569 (tt)
REVERT: D   86 ASP cc_start: 0.8359 (m-30) cc_final: 0.8004 (m-30)
REVERT: D  140 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7476 (mt)
REVERT: D  152 TRP cc_start: 0.8804 (m100) cc_final: 0.8138 (m100)
REVERT: D  215 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8290 (ttp80)
REVERT: A  584 ILE cc_start: 0.8322 (mm) cc_final: 0.8103 (mm)
  outliers start: 10
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1521
  time to fit residues: 17.2733
Evaluate side-chains
  86 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  39 GLN
C 112 GLN
D   6 GLN
D  42 GLN
A 532 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.087922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.076879 restraints weight = 7445.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.078819 restraints weight = 4241.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.080106 restraints weight = 2868.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084   4086  Z= 0.243
  Angle     :  0.635   7.054   5567  Z= 0.319
  Chirality :  0.045   0.161    625
  Planarity :  0.004   0.042    712
  Dihedral  :  4.472  21.719    551
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  3.94 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.42 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.22 (0.36), residues: 508
  helix: -1.23 (2.11), residues: 8
  sheet:  1.16 (0.34), residues: 221
  loop : -0.68 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 106 
 HIS   0.007   0.002   HIS D  80 
 PHE   0.013   0.002   PHE C 153 
 TYR   0.011   0.002   TYR C 182 
 ARG   0.003   0.001   ARG D 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  121)
  hydrogen bonds       : angle       6.74022 (  315)
  SS BOND              : bond        0.00427 (    5)
  SS BOND              : angle       1.53479 (   10)
  covalent geometry    : bond        0.00569 ( 4081)
  covalent geometry    : angle       0.63250 ( 5557)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.472 
Fit side-chains
REVERT: C   91 SER cc_start: 0.8747 (m) cc_final: 0.8293 (p)
REVERT: C  204 VAL cc_start: 0.8399 (p) cc_final: 0.8114 (m)
REVERT: C  215 LYS cc_start: 0.7423 (mmmt) cc_final: 0.6643 (mmmt)
REVERT: D    1 ASP cc_start: 0.8474 (p0) cc_final: 0.8174 (p0)
REVERT: D   32 SER cc_start: 0.8822 (m) cc_final: 0.8460 (p)
REVERT: D   37 MET cc_start: 0.7597 (mmm) cc_final: 0.7161 (tmm)
REVERT: D   86 ASP cc_start: 0.8366 (m-30) cc_final: 0.7996 (m-30)
REVERT: D  140 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7548 (mt)
REVERT: D  152 TRP cc_start: 0.8831 (m100) cc_final: 0.8101 (m100)
REVERT: D  215 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8283 (ttp80)
  outliers start: 9
  outliers final: 8
  residues processed: 83
  average time/residue: 0.1556
  time to fit residues: 16.6601
Evaluate side-chains
  86 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 LEU
Chi-restraints excluded: chain C residue  170 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue  140 LEU
Chi-restraints excluded: chain D residue  179 MET
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain D residue  182 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain A residue  592 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0170
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    0.1980
   chunk 9 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0980
   chunk 33 optimal weight:    0.0470
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.0916

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

Flipped N/Q/H residues before XYZ refinement:
C  39 GLN
D  42 GLN
A 532 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.091479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.080393 restraints weight = 7274.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.082401 restraints weight = 4138.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.083714 restraints weight = 2774.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4086  Z= 0.092
  Angle     :  0.533   7.281   5567  Z= 0.262
  Chirality :  0.043   0.143    625
  Planarity :  0.004   0.038    712
  Dihedral  :  4.110  26.767    551
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.36 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.42 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    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:  0.41 (0.37), residues: 508
  helix: -0.16 (2.54), residues: 7
  sheet:  1.19 (0.34), residues: 220
  loop : -0.46 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  39 
 HIS   0.002   0.001   HIS C 206 
 PHE   0.005   0.001   PHE C  29 
 TYR   0.009   0.001   TYR C  95 
 ARG   0.001   0.000   ARG D  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02658 (  121)
  hydrogen bonds       : angle       6.20683 (  315)
  SS BOND              : bond        0.00378 (    5)
  SS BOND              : angle       1.16608 (   10)
  covalent geometry    : bond        0.00214 ( 4081)
  covalent geometry    : angle       0.53096 ( 5557)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1945.72 seconds
wall clock time: 34 minutes 54.47 seconds (2094.47 seconds total)