Starting phenix.real_space_refine
on Wed Mar 12 17:49:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgl_37225/03_2025/8kgl_37225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgl_37225/03_2025/8kgl_37225.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kgl_37225/03_2025/8kgl_37225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgl_37225/03_2025/8kgl_37225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgl_37225/03_2025/8kgl_37225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgl_37225/03_2025/8kgl_37225.cif"
  }
  resolution = 4.3
  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=   0.001
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    5210      2.51       5
     N    1386      2.21       5
     O    1464      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8084
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 4042
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 468}
    Chain: "B"
      Number of atoms: 4042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 4042
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 468}
  Time building chain proxies: 5.90, per 1000 atoms: 0.73
  Number of scatterers: 8084
  At special positions: 0
  Unit cell: (150.15, 79.95, 108.55, 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    1464      8.00
     N    1386      7.00
     C    5210      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 10 sheets defined
      51.3% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 701 through 707
    Processing helix  chain 'A' and resid 715 through 729
    Processing helix  chain 'A' and resid 737 through 749
    Processing helix  chain 'A' and resid 754 through 765
    Processing helix  chain 'A' and resid 806 through 814
      removed outlier: 4.926A  pdb=" N   THR A 812 " --> pdb=" O   GLU A 808 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 820
      removed outlier: 3.620A  pdb=" N   TRP A 820 " --> pdb=" O   GLU A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 830
      removed outlier: 4.176A  pdb=" N   GLY A 829 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 846
      removed outlier: 3.709A  pdb=" N   ILE A 845 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 877
    Processing helix  chain 'A' and resid 882 through 893
    Processing helix  chain 'A' and resid 942 through 951
    Processing helix  chain 'A' and resid 981 through 990
      removed outlier: 3.741A  pdb=" N   ARG A 985 " --> pdb=" O   ASN A 981 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 997 through 1003
    Processing helix  chain 'A' and resid 1027 through 1070
      removed outlier: 3.639A  pdb=" N   ILE A1031 " --> pdb=" O   THR A1027 " (cutoff:3.500A)
      Proline residue:  A1037  - end of helix
    Processing helix  chain 'A' and resid 1070 through 1075
    Processing helix  chain 'A' and resid 1081 through 1092
    Processing helix  chain 'A' and resid 1098 through 1104
    Processing helix  chain 'A' and resid 1109 through 1116
    Processing helix  chain 'A' and resid 1122 through 1126
    Processing helix  chain 'A' and resid 1134 through 1159
      removed outlier: 3.664A  pdb=" N   LYS A1138 " --> pdb=" O   LEU A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1186
    Processing helix  chain 'B' and resid 702 through 707
    Processing helix  chain 'B' and resid 715 through 729
    Processing helix  chain 'B' and resid 737 through 749
    Processing helix  chain 'B' and resid 754 through 766
    Processing helix  chain 'B' and resid 806 through 814
      removed outlier: 4.990A  pdb=" N   THR B 812 " --> pdb=" O   GLU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 820
      removed outlier: 3.637A  pdb=" N   TRP B 820 " --> pdb=" O   GLU B 817 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 846
      removed outlier: 3.725A  pdb=" N   ILE B 845 " --> pdb=" O   PRO B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 877
    Processing helix  chain 'B' and resid 882 through 893
    Processing helix  chain 'B' and resid 942 through 951
    Processing helix  chain 'B' and resid 981 through 990
      removed outlier: 3.845A  pdb=" N   ARG B 985 " --> pdb=" O   ASN B 981 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 997 through 1003
    Processing helix  chain 'B' and resid 1027 through 1070
      removed outlier: 3.684A  pdb=" N   ILE B1031 " --> pdb=" O   THR B1027 " (cutoff:3.500A)
      Proline residue:  B1037  - end of helix
    Processing helix  chain 'B' and resid 1070 through 1075
    Processing helix  chain 'B' and resid 1081 through 1092
      removed outlier: 3.523A  pdb=" N   ALA B1085 " --> pdb=" O   ASP B1081 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   HIS B1092 " --> pdb=" O   ILE B1088 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1098 through 1104
      removed outlier: 3.522A  pdb=" N   ILE B1102 " --> pdb=" O   ASN B1098 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1109 through 1116
    Processing helix  chain 'B' and resid 1122 through 1126
    Processing helix  chain 'B' and resid 1130 through 1133
      removed outlier: 3.538A  pdb=" N   LEU B1133 " --> pdb=" O   ALA B1130 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1130 through 1133'
    Processing helix  chain 'B' and resid 1134 through 1159
      removed outlier: 4.051A  pdb=" N   LYS B1138 " --> pdb=" O   LEU B1134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1166 through 1188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 779 through 782
    Processing sheet with id=AA2, first strand: chain 'A' and resid 849 through 851
    Processing sheet with id=AA3, first strand: chain 'A' and resid 909 through 913
    Processing sheet with id=AA4, first strand: chain 'A' and resid 923 through 926
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1014 through 1016
    Processing sheet with id=AA6, first strand: chain 'B' and resid 779 through 782
    Processing sheet with id=AA7, first strand: chain 'B' and resid 849 through 851
    Processing sheet with id=AA8, first strand: chain 'B' and resid 909 through 913
    Processing sheet with id=AA9, first strand: chain 'B' and resid 923 through 926
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1014 through 1016

    382 hydrogen bonds defined for protein.
    1077 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2396
        1.34 -     1.45: 1439
        1.45 -     1.57: 4409
        1.57 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 8286
  Sorted by residual:
  bond pdb=" C   TYR A 776 "
       pdb=" N   PRO A 777 "
    ideal  model  delta    sigma   weight residual
    1.332  1.310  0.022 1.12e-02 7.97e+03 3.71e+00
  bond pdb=" N   ARG B1131 "
       pdb=" CA  ARG B1131 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.024 1.35e-02 5.49e+03 3.23e+00
  bond pdb=" CA  GLN A1129 "
       pdb=" C   GLN A1129 "
    ideal  model  delta    sigma   weight residual
    1.523  1.547 -0.023 1.34e-02 5.57e+03 3.05e+00
  bond pdb=" CB  TRP A1170 "
       pdb=" CG  TRP A1170 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.93e+00
  bond pdb=" CB  TRP B1170 "
       pdb=" CG  TRP B1170 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.93e+00
  ... (remaining 8281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 10812
        2.50 -     5.01: 347
        5.01 -     7.51: 31
        7.51 -    10.01: 10
       10.01 -    12.52: 4
  Bond angle restraints: 11204
  Sorted by residual:
  angle pdb=" N   SER B1127 "
        pdb=" CA  SER B1127 "
        pdb=" C   SER B1127 "
      ideal   model   delta    sigma   weight residual
     112.34  122.94  -10.60 1.30e+00 5.92e-01 6.65e+01
  angle pdb=" N   SER A1127 "
        pdb=" CA  SER A1127 "
        pdb=" C   SER A1127 "
      ideal   model   delta    sigma   weight residual
     110.80  123.32  -12.52 2.13e+00 2.20e-01 3.45e+01
  angle pdb=" N   GLY A 786 "
        pdb=" CA  GLY A 786 "
        pdb=" C   GLY A 786 "
      ideal   model   delta    sigma   weight residual
     110.56  116.02   -5.46 1.36e+00 5.41e-01 1.61e+01
  angle pdb=" N   ARG B1131 "
        pdb=" CA  ARG B1131 "
        pdb=" C   ARG B1131 "
      ideal   model   delta    sigma   weight residual
     112.87  117.52   -4.65 1.20e+00 6.94e-01 1.50e+01
  angle pdb=" N   ASN B 851 "
        pdb=" CA  ASN B 851 "
        pdb=" C   ASN B 851 "
      ideal   model   delta    sigma   weight residual
     108.23  114.45   -6.22 1.62e+00 3.81e-01 1.47e+01
  ... (remaining 11199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.17: 4406
       11.17 -    22.35: 500
       22.35 -    33.52: 63
       33.52 -    44.69: 25
       44.69 -    55.86: 4
  Dihedral angle restraints: 4998
    sinusoidal: 2088
      harmonic: 2910
  Sorted by residual:
  dihedral pdb=" CA  GLN B1129 "
           pdb=" C   GLN B1129 "
           pdb=" N   ALA B1130 "
           pdb=" CA  ALA B1130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -124.14  -55.86     0      5.00e+00 4.00e-02 1.25e+02
  dihedral pdb=" CA  ILE A1125 "
           pdb=" C   ILE A1125 "
           pdb=" N   LEU A1126 "
           pdb=" CA  LEU A1126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.47  -44.53     0      5.00e+00 4.00e-02 7.93e+01
  dihedral pdb=" CA  LEU B1126 "
           pdb=" C   LEU B1126 "
           pdb=" N   SER B1127 "
           pdb=" CA  SER B1127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -135.95  -44.05     0      5.00e+00 4.00e-02 7.76e+01
  ... (remaining 4995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 791
       0.046 -    0.092: 296
       0.092 -    0.139: 94
       0.139 -    0.185: 14
       0.185 -    0.231: 5
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CA  SER B1127 "
            pdb=" N   SER B1127 "
            pdb=" C   SER B1127 "
            pdb=" CB  SER B1127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE B1023 "
            pdb=" CA  ILE B1023 "
            pdb=" CG1 ILE B1023 "
            pdb=" CG2 ILE B1023 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CB  ILE A1023 "
            pdb=" CA  ILE A1023 "
            pdb=" CG1 ILE A1023 "
            pdb=" CG2 ILE A1023 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1197 not shown)

  Planarity restraints: 1432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B1170 "    0.031 2.00e-02 2.50e+03   3.18e-02 2.53e+01
        pdb=" CG  TRP B1170 "   -0.084 2.00e-02 2.50e+03
        pdb=" CD1 TRP B1170 "    0.045 2.00e-02 2.50e+03
        pdb=" CD2 TRP B1170 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B1170 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B1170 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B1170 "    0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP B1170 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1170 "   -0.030 2.00e-02 2.50e+03   3.09e-02 2.39e+01
        pdb=" CG  TRP A1170 "    0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1170 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1170 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1170 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1170 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1170 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1170 "   -0.006 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1170 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B1129 "    0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   GLN B1129 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLN B1129 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ALA B1130 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1429 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2152
        2.80 -     3.33: 7635
        3.33 -     3.85: 13569
        3.85 -     4.38: 15627
        4.38 -     4.90: 24977
  Nonbonded interactions: 63960
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B1043 "
            pdb=" OE1 GLU B1173 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A1043 "
            pdb=" OE1 GLU A1173 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   PHE B 809 "
            pdb=" OG1 THR B 812 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   PHE A 809 "
            pdb=" OG1 THR A 812 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG  SER A 787 "
            pdb=" OD2 ASP A 794 "
     model   vdw
     2.292 3.040
  ... (remaining 63955 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.580
  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:          0.430
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.580
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
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      :  0.007   0.055   8286  Z= 0.463
  Angle     :  1.064  12.515  11204  Z= 0.596
  Chirality :  0.054   0.231   1200
  Planarity :  0.009   0.073   1432
  Dihedral  :  9.436  55.861   3130
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.85 %

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: -3.21 (0.24), residues: 980
  helix: -1.63 (0.19), residues: 436
  sheet: -2.45 (0.49), residues: 112
  loop : -2.47 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.084   0.007   TRP B1170 
 HIS   0.007   0.002   HIS B 752 
 PHE   0.024   0.003   PHE B 750 
 TYR   0.032   0.003   TYR B 917 
 ARG   0.008   0.001   ARG B 940 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  843 LEU cc_start: 0.9058 (tp) cc_final: 0.8791 (tt)
REVERT: A  847 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7361 (mt-10)
REVERT: A  954 SER cc_start: 0.8457 (m) cc_final: 0.8253 (p)
REVERT: A  957 MET cc_start: 0.9455 (mmm) cc_final: 0.9068 (mmm)
REVERT: A  966 TYR cc_start: 0.6365 (m-80) cc_final: 0.6058 (m-80)
REVERT: A 1106 GLU cc_start: 0.8215 (pm20) cc_final: 0.7934 (pm20)
REVERT: A 1169 VAL cc_start: 0.9403 (t) cc_final: 0.9083 (t)
REVERT: B  843 LEU cc_start: 0.9001 (tp) cc_final: 0.8741 (tt)
REVERT: B  847 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7092 (mt-10)
REVERT: B  897 LEU cc_start: 0.7919 (mt) cc_final: 0.7414 (mp)
REVERT: B  954 SER cc_start: 0.8554 (m) cc_final: 0.8350 (p)
REVERT: B  957 MET cc_start: 0.9477 (mmm) cc_final: 0.9085 (mmm)
REVERT: B  966 TYR cc_start: 0.6621 (m-80) cc_final: 0.6228 (m-80)
REVERT: B 1106 GLU cc_start: 0.8184 (pm20) cc_final: 0.7917 (pm20)
REVERT: B 1132 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7549 (tp30)
REVERT: B 1148 MET cc_start: 0.7242 (mtm) cc_final: 0.6627 (ptm)
REVERT: B 1169 VAL cc_start: 0.9387 (t) cc_final: 0.9036 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.2387
  time to fit residues: 62.7907
Evaluate side-chains
  107 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:   20.0000
   chunk 50 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 76 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.3980
   chunk 57 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
A 804 GLN
A 864 GLN
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1012 HIS
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 789 HIS
B 804 GLN
B 864 GLN
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1012 HIS
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.085996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.069085 restraints weight = 37382.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.071200 restraints weight = 23691.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.072760 restraints weight = 16953.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8286  Z= 0.174
  Angle     :  0.625   9.423  11204  Z= 0.336
  Chirality :  0.042   0.153   1200
  Planarity :  0.006   0.050   1432
  Dihedral  :  6.636  46.959   1104
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.85 %

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: -1.79 (0.26), residues: 980
  helix:  0.13 (0.24), residues: 428
  sheet: -2.16 (0.48), residues: 112
  loop : -2.28 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A1170 
 HIS   0.004   0.001   HIS B 883 
 PHE   0.008   0.001   PHE B 750 
 TYR   0.015   0.002   TYR B 917 
 ARG   0.009   0.001   ARG B 716 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8340 (mpp) cc_final: 0.7849 (mpp)
REVERT: A  846 MET cc_start: 0.8382 (ttm) cc_final: 0.8030 (ttm)
REVERT: A  957 MET cc_start: 0.9506 (mmm) cc_final: 0.9108 (mmm)
REVERT: A  966 TYR cc_start: 0.6169 (m-80) cc_final: 0.5943 (m-80)
REVERT: A 1060 MET cc_start: 0.7642 (ttp) cc_final: 0.7319 (tmm)
REVERT: A 1128 LEU cc_start: 0.8922 (mt) cc_final: 0.8651 (mt)
REVERT: A 1148 MET cc_start: 0.7470 (mtp) cc_final: 0.7206 (ptt)
REVERT: A 1153 ASP cc_start: 0.8913 (m-30) cc_final: 0.8689 (m-30)
REVERT: A 1169 VAL cc_start: 0.9465 (t) cc_final: 0.8932 (p)
REVERT: B  714 MET cc_start: 0.8404 (mpp) cc_final: 0.7913 (mpp)
REVERT: B  846 MET cc_start: 0.8355 (ttm) cc_final: 0.8035 (ttm)
REVERT: B  905 ASN cc_start: 0.8748 (m110) cc_final: 0.8539 (m110)
REVERT: B  957 MET cc_start: 0.9514 (mmm) cc_final: 0.9114 (mmm)
REVERT: B  966 TYR cc_start: 0.6394 (m-80) cc_final: 0.6091 (m-80)
REVERT: B 1060 MET cc_start: 0.7602 (ttp) cc_final: 0.7312 (tmm)
REVERT: B 1112 GLU cc_start: 0.9189 (mp0) cc_final: 0.8735 (mp0)
REVERT: B 1153 ASP cc_start: 0.8908 (m-30) cc_final: 0.8698 (m-30)
REVERT: B 1169 VAL cc_start: 0.9472 (t) cc_final: 0.9059 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2077
  time to fit residues: 45.3747
Evaluate side-chains
  100 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    0.4980
   chunk 60 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.086874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.069531 restraints weight = 37806.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.071674 restraints weight = 24194.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.073286 restraints weight = 17483.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8286  Z= 0.159
  Angle     :  0.580   9.052  11204  Z= 0.309
  Chirality :  0.041   0.155   1200
  Planarity :  0.005   0.047   1432
  Dihedral  :  5.944  46.721   1104
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.26 %
    Favored  : 98.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.27), residues: 980
  helix:  0.65 (0.24), residues: 448
  sheet: -1.83 (0.46), residues: 122
  loop : -2.00 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1170 
 HIS   0.002   0.001   HIS A1092 
 PHE   0.016   0.001   PHE A 710 
 TYR   0.019   0.001   TYR A 769 
 ARG   0.003   0.000   ARG A 716 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8428 (mpp) cc_final: 0.7926 (mpp)
REVERT: A  856 TRP cc_start: 0.4660 (p-90) cc_final: 0.4198 (p-90)
REVERT: A  957 MET cc_start: 0.9524 (mmm) cc_final: 0.9102 (mmm)
REVERT: A  966 TYR cc_start: 0.6180 (m-80) cc_final: 0.5972 (m-80)
REVERT: A 1023 ILE cc_start: 0.9114 (tt) cc_final: 0.8894 (tt)
REVERT: A 1060 MET cc_start: 0.7672 (ttp) cc_final: 0.7426 (tmm)
REVERT: A 1153 ASP cc_start: 0.8930 (m-30) cc_final: 0.8696 (m-30)
REVERT: A 1169 VAL cc_start: 0.9406 (t) cc_final: 0.9085 (p)
REVERT: B  710 PHE cc_start: 0.9191 (p90) cc_final: 0.8937 (p90)
REVERT: B  714 MET cc_start: 0.8429 (mpp) cc_final: 0.7950 (mpp)
REVERT: B  957 MET cc_start: 0.9506 (mmm) cc_final: 0.9079 (mmm)
REVERT: B  966 TYR cc_start: 0.6451 (m-80) cc_final: 0.6171 (m-80)
REVERT: B 1023 ILE cc_start: 0.9056 (tt) cc_final: 0.8747 (tt)
REVERT: B 1038 TYR cc_start: 0.8859 (m-10) cc_final: 0.8625 (m-10)
REVERT: B 1060 MET cc_start: 0.7544 (ttp) cc_final: 0.7297 (tmm)
REVERT: B 1148 MET cc_start: 0.7130 (mtm) cc_final: 0.6609 (ttp)
REVERT: B 1153 ASP cc_start: 0.8931 (m-30) cc_final: 0.8717 (m-30)
REVERT: B 1169 VAL cc_start: 0.9444 (t) cc_final: 0.8992 (p)
REVERT: B 1173 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8975 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2266
  time to fit residues: 44.1703
Evaluate side-chains
  101 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 80 optimal weight:   20.0000
   chunk 21 optimal weight:    0.4980
   chunk 67 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 774 HIS
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 774 HIS
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** 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 = 0.3946 r_free = 0.3946 target = 0.083473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.066710 restraints weight = 37852.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.068776 restraints weight = 23937.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.070188 restraints weight = 17133.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8286  Z= 0.223
  Angle     :  0.604   9.275  11204  Z= 0.322
  Chirality :  0.042   0.152   1200
  Planarity :  0.005   0.042   1432
  Dihedral  :  5.944  48.608   1104
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

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: -0.93 (0.27), residues: 980
  helix:  0.92 (0.23), residues: 450
  sheet: -1.71 (0.47), residues: 122
  loop : -2.05 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B1170 
 HIS   0.004   0.001   HIS A1099 
 PHE   0.025   0.002   PHE A1025 
 TYR   0.018   0.002   TYR A 858 
 ARG   0.013   0.001   ARG B1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  846 MET cc_start: 0.8361 (ttm) cc_final: 0.8010 (ttm)
REVERT: A  856 TRP cc_start: 0.4649 (p-90) cc_final: 0.4406 (p-90)
REVERT: A  957 MET cc_start: 0.9529 (mmm) cc_final: 0.9130 (mmm)
REVERT: A  966 TYR cc_start: 0.6126 (m-80) cc_final: 0.5895 (m-80)
REVERT: A 1102 ILE cc_start: 0.8907 (pt) cc_final: 0.8701 (pt)
REVERT: A 1153 ASP cc_start: 0.8997 (m-30) cc_final: 0.8776 (m-30)
REVERT: A 1169 VAL cc_start: 0.9508 (t) cc_final: 0.8843 (t)
REVERT: A 1173 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8850 (mt-10)
REVERT: B  833 GLU cc_start: 0.8452 (pt0) cc_final: 0.8014 (pt0)
REVERT: B  846 MET cc_start: 0.8393 (ttm) cc_final: 0.8014 (ttm)
REVERT: B  885 LEU cc_start: 0.9393 (mt) cc_final: 0.9085 (mt)
REVERT: B  905 ASN cc_start: 0.8678 (m110) cc_final: 0.8398 (m-40)
REVERT: B  957 MET cc_start: 0.9517 (mmm) cc_final: 0.9112 (mmm)
REVERT: B  966 TYR cc_start: 0.6371 (m-80) cc_final: 0.6073 (m-80)
REVERT: B 1038 TYR cc_start: 0.8859 (m-10) cc_final: 0.8579 (m-10)
REVERT: B 1060 MET cc_start: 0.7645 (ttp) cc_final: 0.7230 (tmm)
REVERT: B 1148 MET cc_start: 0.7251 (mtm) cc_final: 0.7036 (mtp)
REVERT: B 1153 ASP cc_start: 0.8986 (m-30) cc_final: 0.8763 (m-30)
REVERT: B 1169 VAL cc_start: 0.9371 (t) cc_final: 0.8905 (t)
REVERT: B 1173 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8961 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2850
  time to fit residues: 51.3998
Evaluate side-chains
  98 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0970
   chunk 25 optimal weight:   20.0000
   chunk 75 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.084543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.067404 restraints weight = 37492.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.069409 restraints weight = 24316.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.070878 restraints weight = 17673.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8286  Z= 0.187
  Angle     :  0.570   8.954  11204  Z= 0.303
  Chirality :  0.042   0.167   1200
  Planarity :  0.005   0.066   1432
  Dihedral  :  5.712  48.881   1104
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

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: -0.62 (0.27), residues: 980
  helix:  1.27 (0.24), residues: 448
  sheet: -1.71 (0.48), residues: 122
  loop : -1.93 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B1189 
 HIS   0.002   0.001   HIS B 753 
 PHE   0.011   0.001   PHE A1025 
 TYR   0.021   0.002   TYR A 769 
 ARG   0.005   0.000   ARG A1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  846 MET cc_start: 0.8316 (ttm) cc_final: 0.7976 (ttm)
REVERT: A  856 TRP cc_start: 0.4565 (p-90) cc_final: 0.4270 (p-90)
REVERT: A  882 LYS cc_start: 0.8783 (pttt) cc_final: 0.8499 (ptpp)
REVERT: A  957 MET cc_start: 0.9531 (mmm) cc_final: 0.9116 (mmm)
REVERT: A  966 TYR cc_start: 0.6127 (m-80) cc_final: 0.5899 (m-80)
REVERT: A 1038 TYR cc_start: 0.8810 (m-10) cc_final: 0.8582 (m-10)
REVERT: A 1132 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7784 (tp30)
REVERT: A 1153 ASP cc_start: 0.8994 (m-30) cc_final: 0.8786 (m-30)
REVERT: A 1169 VAL cc_start: 0.9360 (t) cc_final: 0.8928 (t)
REVERT: A 1173 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8708 (mt-10)
REVERT: B  833 GLU cc_start: 0.8422 (pt0) cc_final: 0.8069 (pt0)
REVERT: B  846 MET cc_start: 0.8367 (ttm) cc_final: 0.8014 (ttm)
REVERT: B  856 TRP cc_start: 0.3858 (p-90) cc_final: 0.3007 (p-90)
REVERT: B  885 LEU cc_start: 0.9295 (mt) cc_final: 0.9050 (mt)
REVERT: B  905 ASN cc_start: 0.8697 (m110) cc_final: 0.8417 (m-40)
REVERT: B  957 MET cc_start: 0.9520 (mmm) cc_final: 0.9102 (mmm)
REVERT: B  966 TYR cc_start: 0.6384 (m-80) cc_final: 0.6070 (m-80)
REVERT: B 1038 TYR cc_start: 0.8805 (m-10) cc_final: 0.8528 (m-10)
REVERT: B 1060 MET cc_start: 0.7606 (ttp) cc_final: 0.7289 (tmm)
REVERT: B 1148 MET cc_start: 0.7283 (mtm) cc_final: 0.7072 (mtp)
REVERT: B 1153 ASP cc_start: 0.8976 (m-30) cc_final: 0.8762 (m-30)
REVERT: B 1169 VAL cc_start: 0.9340 (t) cc_final: 0.8939 (t)
REVERT: B 1173 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8939 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1935
  time to fit residues: 37.4660
Evaluate side-chains
  99 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 21 optimal weight:    7.9990
   chunk 85 optimal weight:    5.9990
   chunk 23 optimal weight:   40.0000
   chunk 53 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 71 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0670
   chunk 14 optimal weight:    0.0370
   chunk 37 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    1.6202

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 HIS
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.084066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.067639 restraints weight = 37314.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.069594 restraints weight = 23917.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.071063 restraints weight = 17295.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8286  Z= 0.180
  Angle     :  0.565   9.508  11204  Z= 0.300
  Chirality :  0.041   0.181   1200
  Planarity :  0.005   0.070   1432
  Dihedral  :  5.505  44.593   1104
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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: -0.42 (0.28), residues: 980
  helix:  1.41 (0.24), residues: 448
  sheet: -1.65 (0.49), residues: 122
  loop : -1.79 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B1189 
 HIS   0.002   0.001   HIS A 753 
 PHE   0.016   0.001   PHE A 739 
 TYR   0.014   0.001   TYR A1043 
 ARG   0.003   0.000   ARG A1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8814 (p0) cc_final: 0.6692 (p0)
REVERT: A  714 MET cc_start: 0.8270 (mpp) cc_final: 0.7823 (mpp)
REVERT: A  846 MET cc_start: 0.8332 (ttm) cc_final: 0.7996 (ttm)
REVERT: A  856 TRP cc_start: 0.4429 (p-90) cc_final: 0.4107 (p-90)
REVERT: A  882 LYS cc_start: 0.8801 (pttt) cc_final: 0.8496 (ptpp)
REVERT: A  956 ARG cc_start: 0.9158 (mmt90) cc_final: 0.8901 (mmt90)
REVERT: A  957 MET cc_start: 0.9546 (mmm) cc_final: 0.9125 (mmm)
REVERT: A  966 TYR cc_start: 0.6155 (m-80) cc_final: 0.5935 (m-80)
REVERT: A 1060 MET cc_start: 0.8129 (tmm) cc_final: 0.7790 (tmm)
REVERT: A 1153 ASP cc_start: 0.9005 (m-30) cc_final: 0.8789 (m-30)
REVERT: B  714 MET cc_start: 0.8300 (mpp) cc_final: 0.8002 (mpp)
REVERT: B  833 GLU cc_start: 0.8385 (pt0) cc_final: 0.8043 (pt0)
REVERT: B  846 MET cc_start: 0.8360 (ttm) cc_final: 0.8005 (ttm)
REVERT: B  856 TRP cc_start: 0.3817 (p-90) cc_final: 0.3018 (p-90)
REVERT: B  905 ASN cc_start: 0.8778 (m110) cc_final: 0.8489 (m-40)
REVERT: B  957 MET cc_start: 0.9519 (mmm) cc_final: 0.9074 (mmm)
REVERT: B  966 TYR cc_start: 0.6360 (m-80) cc_final: 0.6050 (m-80)
REVERT: B 1038 TYR cc_start: 0.8765 (m-10) cc_final: 0.8486 (m-10)
REVERT: B 1060 MET cc_start: 0.7637 (ttp) cc_final: 0.7304 (tmm)
REVERT: B 1128 LEU cc_start: 0.8919 (mt) cc_final: 0.8647 (mt)
REVERT: B 1148 MET cc_start: 0.7267 (mtm) cc_final: 0.7045 (mtp)
REVERT: B 1153 ASP cc_start: 0.8966 (m-30) cc_final: 0.8758 (m-30)
REVERT: B 1173 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8936 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1538
  time to fit residues: 28.6086
Evaluate side-chains
  98 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0170
   chunk 3 optimal weight:    8.9990
   chunk 37 optimal weight:    0.2980
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:   10.0000
   chunk 71 optimal weight:    0.0000
   chunk 46 optimal weight:    0.0970
   chunk 40 optimal weight:    9.9990
   overall best weight:    0.2820

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

Flipped N/Q/H residues before XYZ refinement:
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 HIS
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.088040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.070588 restraints weight = 36878.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.072611 restraints weight = 24240.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.074200 restraints weight = 17835.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8286  Z= 0.134
  Angle     :  0.540  12.897  11204  Z= 0.283
  Chirality :  0.041   0.278   1200
  Planarity :  0.005   0.046   1432
  Dihedral  :  5.205  38.517   1104
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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: -0.03 (0.28), residues: 980
  helix:  1.74 (0.24), residues: 448
  sheet: -1.41 (0.50), residues: 122
  loop : -1.61 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1189 
 HIS   0.005   0.001   HIS A 892 
 PHE   0.015   0.001   PHE A 739 
 TYR   0.020   0.001   TYR A 769 
 ARG   0.003   0.000   ARG B 734 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8897 (p0) cc_final: 0.6480 (p0)
REVERT: A  714 MET cc_start: 0.8247 (mpp) cc_final: 0.7748 (mpp)
REVERT: A  737 LYS cc_start: 0.8886 (mttt) cc_final: 0.8396 (mtpp)
REVERT: A  833 GLU cc_start: 0.8500 (pt0) cc_final: 0.8231 (pt0)
REVERT: A  848 TYR cc_start: 0.7007 (m-10) cc_final: 0.6659 (m-10)
REVERT: A  856 TRP cc_start: 0.4387 (p-90) cc_final: 0.4100 (p-90)
REVERT: A  882 LYS cc_start: 0.8783 (pttt) cc_final: 0.8422 (ptpp)
REVERT: A  957 MET cc_start: 0.9535 (mmm) cc_final: 0.9118 (mmm)
REVERT: A 1038 TYR cc_start: 0.8734 (m-10) cc_final: 0.8481 (m-10)
REVERT: A 1153 ASP cc_start: 0.8970 (m-30) cc_final: 0.8761 (m-30)
REVERT: A 1169 VAL cc_start: 0.9414 (t) cc_final: 0.9041 (p)
REVERT: A 1173 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8760 (mt-10)
REVERT: B  712 ASP cc_start: 0.8908 (p0) cc_final: 0.6593 (p0)
REVERT: B  714 MET cc_start: 0.8244 (mpp) cc_final: 0.7800 (mpp)
REVERT: B  833 GLU cc_start: 0.8394 (pt0) cc_final: 0.8095 (pt0)
REVERT: B  846 MET cc_start: 0.8317 (ttm) cc_final: 0.7980 (ttm)
REVERT: B  856 TRP cc_start: 0.3829 (p-90) cc_final: 0.3128 (p-90)
REVERT: B  905 ASN cc_start: 0.8783 (m110) cc_final: 0.8490 (m-40)
REVERT: B  917 TYR cc_start: 0.8768 (m-10) cc_final: 0.8424 (m-80)
REVERT: B  957 MET cc_start: 0.9516 (mmm) cc_final: 0.9047 (mmm)
REVERT: B 1023 ILE cc_start: 0.9130 (tt) cc_final: 0.8883 (tt)
REVERT: B 1038 TYR cc_start: 0.8729 (m-10) cc_final: 0.8480 (m-10)
REVERT: B 1148 MET cc_start: 0.7180 (mtm) cc_final: 0.6970 (mtp)
REVERT: B 1153 ASP cc_start: 0.8912 (m-30) cc_final: 0.8670 (m-30)
REVERT: B 1169 VAL cc_start: 0.9330 (t) cc_final: 0.8855 (t)
REVERT: B 1173 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8991 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.2902
  time to fit residues: 57.4938
Evaluate side-chains
  102 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 64 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 78 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3844

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 905 ASN
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.086022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.068906 restraints weight = 38011.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.070988 restraints weight = 24422.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.072498 restraints weight = 17689.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8286  Z= 0.171
  Angle     :  0.561  11.803  11204  Z= 0.295
  Chirality :  0.041   0.242   1200
  Planarity :  0.004   0.037   1432
  Dihedral  :  5.220  45.554   1104
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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:  0.09 (0.28), residues: 980
  helix:  1.80 (0.24), residues: 450
  sheet: -1.30 (0.50), residues: 122
  loop : -1.54 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B1189 
 HIS   0.004   0.001   HIS A 892 
 PHE   0.017   0.001   PHE B 710 
 TYR   0.014   0.001   TYR B1043 
 ARG   0.004   0.000   ARG A1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8980 (p0) cc_final: 0.6652 (p0)
REVERT: A  714 MET cc_start: 0.8298 (mpp) cc_final: 0.7770 (mpp)
REVERT: A  737 LYS cc_start: 0.8871 (mttt) cc_final: 0.8564 (mtpt)
REVERT: A  818 ASP cc_start: 0.8290 (m-30) cc_final: 0.8067 (m-30)
REVERT: A  833 GLU cc_start: 0.8506 (pt0) cc_final: 0.8257 (pt0)
REVERT: A  846 MET cc_start: 0.8279 (ttp) cc_final: 0.7964 (ttm)
REVERT: A  848 TYR cc_start: 0.7233 (m-10) cc_final: 0.6990 (m-10)
REVERT: A  856 TRP cc_start: 0.4329 (p-90) cc_final: 0.3909 (p-90)
REVERT: A  882 LYS cc_start: 0.8913 (ptpt) cc_final: 0.8660 (ptpp)
REVERT: A  957 MET cc_start: 0.9537 (mmm) cc_final: 0.9101 (mmm)
REVERT: A 1060 MET cc_start: 0.7898 (tmm) cc_final: 0.7381 (tmm)
REVERT: A 1153 ASP cc_start: 0.8960 (m-30) cc_final: 0.8759 (m-30)
REVERT: A 1169 VAL cc_start: 0.9375 (t) cc_final: 0.8859 (t)
REVERT: A 1173 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8816 (mt-10)
REVERT: B  712 ASP cc_start: 0.8962 (p0) cc_final: 0.6717 (p0)
REVERT: B  714 MET cc_start: 0.8275 (mpp) cc_final: 0.7828 (mpp)
REVERT: B  833 GLU cc_start: 0.8463 (pt0) cc_final: 0.8063 (tt0)
REVERT: B  856 TRP cc_start: 0.3826 (p-90) cc_final: 0.3108 (p-90)
REVERT: B  905 ASN cc_start: 0.8833 (m110) cc_final: 0.8538 (m-40)
REVERT: B  917 TYR cc_start: 0.8838 (m-10) cc_final: 0.8473 (m-80)
REVERT: B  957 MET cc_start: 0.9509 (mmm) cc_final: 0.9057 (mmm)
REVERT: B  966 TYR cc_start: 0.5349 (m-80) cc_final: 0.5086 (m-80)
REVERT: B 1038 TYR cc_start: 0.8735 (m-10) cc_final: 0.8449 (m-10)
REVERT: B 1148 MET cc_start: 0.7314 (mtm) cc_final: 0.7069 (mtp)
REVERT: B 1153 ASP cc_start: 0.8949 (m-30) cc_final: 0.8738 (m-30)
REVERT: B 1169 VAL cc_start: 0.9455 (t) cc_final: 0.8831 (t)
REVERT: B 1173 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9066 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1546
  time to fit residues: 30.2868
Evaluate side-chains
  93 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 53 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 85 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 774 HIS
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 HIS
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1075 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.086516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.069657 restraints weight = 36863.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.071734 restraints weight = 23647.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.073270 restraints weight = 16979.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8286  Z= 0.158
  Angle     :  0.557  11.532  11204  Z= 0.291
  Chirality :  0.041   0.232   1200
  Planarity :  0.004   0.036   1432
  Dihedral  :  5.153  43.364   1104
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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:  0.13 (0.28), residues: 980
  helix:  1.84 (0.24), residues: 448
  sheet: -1.19 (0.50), residues: 122
  loop : -1.54 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A 892 
 PHE   0.015   0.001   PHE B 710 
 TYR   0.022   0.001   TYR A 769 
 ARG   0.004   0.000   ARG A1039 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.9012 (p0) cc_final: 0.6625 (p0)
REVERT: A  714 MET cc_start: 0.8299 (mpp) cc_final: 0.7733 (mpp)
REVERT: A  737 LYS cc_start: 0.8838 (mttt) cc_final: 0.8574 (mtpt)
REVERT: A  818 ASP cc_start: 0.8284 (m-30) cc_final: 0.8083 (m-30)
REVERT: A  833 GLU cc_start: 0.8474 (pt0) cc_final: 0.8173 (tt0)
REVERT: A  846 MET cc_start: 0.8240 (ttp) cc_final: 0.7968 (ttm)
REVERT: A  856 TRP cc_start: 0.4101 (p-90) cc_final: 0.3821 (p-90)
REVERT: A  882 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8679 (ptpp)
REVERT: A  905 ASN cc_start: 0.8711 (m110) cc_final: 0.8356 (m-40)
REVERT: A  957 MET cc_start: 0.9532 (mmm) cc_final: 0.9090 (mmm)
REVERT: A  966 TYR cc_start: 0.6399 (m-10) cc_final: 0.6178 (m-80)
REVERT: A 1060 MET cc_start: 0.7957 (tmm) cc_final: 0.7613 (tmm)
REVERT: A 1148 MET cc_start: 0.7344 (ttp) cc_final: 0.7115 (tmm)
REVERT: A 1169 VAL cc_start: 0.9358 (t) cc_final: 0.8849 (t)
REVERT: A 1173 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8804 (mt-10)
REVERT: B  712 ASP cc_start: 0.9000 (p0) cc_final: 0.6643 (p0)
REVERT: B  714 MET cc_start: 0.8279 (mpp) cc_final: 0.7802 (mpp)
REVERT: B  833 GLU cc_start: 0.8382 (pt0) cc_final: 0.8037 (tt0)
REVERT: B  856 TRP cc_start: 0.3681 (p-90) cc_final: 0.2937 (p-90)
REVERT: B  905 ASN cc_start: 0.8800 (m110) cc_final: 0.8534 (m-40)
REVERT: B  917 TYR cc_start: 0.8797 (m-10) cc_final: 0.8431 (m-80)
REVERT: B  957 MET cc_start: 0.9522 (mmm) cc_final: 0.9026 (mmm)
REVERT: B  966 TYR cc_start: 0.5481 (m-80) cc_final: 0.5193 (m-80)
REVERT: B 1038 TYR cc_start: 0.8712 (m-10) cc_final: 0.8442 (m-10)
REVERT: B 1128 LEU cc_start: 0.8709 (mm) cc_final: 0.8293 (mm)
REVERT: B 1148 MET cc_start: 0.7290 (mtm) cc_final: 0.7019 (mtp)
REVERT: B 1153 ASP cc_start: 0.8932 (m-30) cc_final: 0.8718 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1750
  time to fit residues: 34.7386
Evaluate side-chains
  96 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    0.0030
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   chunk 94 optimal weight:    0.8980
   chunk 88 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0040
   chunk 86 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0050
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.1816

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 774 HIS
A 887 HIS
B 774 HIS
** B 887 HIS ** 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 = 0.4055 r_free = 0.4055 target = 0.088700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.071283 restraints weight = 36748.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.073442 restraints weight = 23794.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.074782 restraints weight = 17212.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8286  Z= 0.140
  Angle     :  0.556   9.858  11204  Z= 0.288
  Chirality :  0.041   0.168   1200
  Planarity :  0.004   0.035   1432
  Dihedral  :  5.050  44.068   1104
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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 (0.28), residues: 980
  helix:  1.93 (0.24), residues: 454
  sheet: -0.93 (0.51), residues: 118
  loop : -1.58 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1189 
 HIS   0.004   0.001   HIS A 892 
 PHE   0.014   0.001   PHE B 710 
 TYR   0.012   0.001   TYR B1043 
 ARG   0.003   0.000   ARG B 734 

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.9027 (p0) cc_final: 0.6458 (p0)
REVERT: A  714 MET cc_start: 0.8261 (mpp) cc_final: 0.7665 (mpp)
REVERT: A  737 LYS cc_start: 0.8845 (mttt) cc_final: 0.8489 (mtpp)
REVERT: A  818 ASP cc_start: 0.8357 (m-30) cc_final: 0.8100 (m-30)
REVERT: A  833 GLU cc_start: 0.8434 (pt0) cc_final: 0.8106 (tt0)
REVERT: A  846 MET cc_start: 0.8159 (ttp) cc_final: 0.7940 (ttm)
REVERT: A  882 LYS cc_start: 0.8948 (ptpt) cc_final: 0.8700 (ptpp)
REVERT: A  905 ASN cc_start: 0.8715 (m110) cc_final: 0.8340 (m-40)
REVERT: A  917 TYR cc_start: 0.8793 (m-10) cc_final: 0.8591 (m-80)
REVERT: A  957 MET cc_start: 0.9533 (mmm) cc_final: 0.9112 (mmm)
REVERT: A  966 TYR cc_start: 0.6300 (m-10) cc_final: 0.6088 (m-80)
REVERT: A 1038 TYR cc_start: 0.8737 (m-80) cc_final: 0.8490 (m-10)
REVERT: A 1060 MET cc_start: 0.7933 (tmm) cc_final: 0.7671 (tmm)
REVERT: A 1125 ILE cc_start: 0.8720 (mt) cc_final: 0.8372 (tp)
REVERT: A 1148 MET cc_start: 0.7292 (ttp) cc_final: 0.7034 (tmm)
REVERT: A 1169 VAL cc_start: 0.9401 (t) cc_final: 0.9118 (p)
REVERT: A 1173 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8858 (mt-10)
REVERT: B  712 ASP cc_start: 0.9016 (p0) cc_final: 0.6607 (p0)
REVERT: B  714 MET cc_start: 0.8194 (mpp) cc_final: 0.7730 (mpp)
REVERT: B  818 ASP cc_start: 0.8300 (m-30) cc_final: 0.8023 (m-30)
REVERT: B  833 GLU cc_start: 0.8294 (pt0) cc_final: 0.7991 (tt0)
REVERT: B  846 MET cc_start: 0.8221 (ttp) cc_final: 0.7930 (tmm)
REVERT: B  856 TRP cc_start: 0.3717 (p-90) cc_final: 0.2956 (p-90)
REVERT: B  905 ASN cc_start: 0.8856 (m110) cc_final: 0.8602 (m-40)
REVERT: B  917 TYR cc_start: 0.8692 (m-10) cc_final: 0.8325 (m-80)
REVERT: B  957 MET cc_start: 0.9513 (mmm) cc_final: 0.9061 (mmm)
REVERT: B  966 TYR cc_start: 0.5429 (m-80) cc_final: 0.5139 (m-80)
REVERT: B 1038 TYR cc_start: 0.8706 (m-10) cc_final: 0.8430 (m-10)
REVERT: B 1060 MET cc_start: 0.7764 (tmm) cc_final: 0.7502 (tmm)
REVERT: B 1128 LEU cc_start: 0.8623 (mm) cc_final: 0.8046 (mm)
REVERT: B 1153 ASP cc_start: 0.8927 (m-30) cc_final: 0.8693 (m-30)
REVERT: B 1169 VAL cc_start: 0.9429 (t) cc_final: 0.8797 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1828
  time to fit residues: 35.6574
Evaluate side-chains
  99 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 19 optimal weight:   20.0000
   chunk 71 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0050
   chunk 39 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    9.9990
   chunk 56 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 774 HIS
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1192 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.083942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.067443 restraints weight = 38598.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.069475 restraints weight = 24665.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.070921 restraints weight = 17726.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.5026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8286  Z= 0.254
  Angle     :  0.630   9.770  11204  Z= 0.333
  Chirality :  0.044   0.202   1200
  Planarity :  0.005   0.054   1432
  Dihedral  :  5.276  45.416   1104
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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:  0.08 (0.28), residues: 980
  helix:  1.79 (0.24), residues: 454
  sheet: -0.06 (0.56), residues: 98
  loop : -1.94 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B1170 
 HIS   0.009   0.001   HIS B1099 
 PHE   0.012   0.002   PHE A 739 
 TYR   0.029   0.002   TYR A 769 
 ARG   0.009   0.001   ARG B1140 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3198.88 seconds
wall clock time: 58 minutes 30.09 seconds (3510.09 seconds total)