Starting phenix.real_space_refine
on Wed Feb 12 17:15:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgl_37225/02_2025/8kgl_37225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgl_37225/02_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_37225/02_2025/8kgl_37225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgl_37225/02_2025/8kgl_37225.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgl_37225/02_2025/8kgl_37225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgl_37225/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.76, per 1000 atoms: 0.71
  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: 1.96
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.85
  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: 2.20

  Time building geometry restraints manager: 2.27 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:             3.000
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     21.390
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.000
-------------------------------------------------------------------------------
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  : 0.920 
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: 0.2441
  time to fit residues: 63.9783
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  : 1.041 
-------------------------------------------------------------------------------
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 = 0.069082 restraints weight = 37382.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.071226 restraints weight = 23706.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.072781 restraints weight = 16897.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
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  : 0.942 
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: 0.8381 (ttm) cc_final: 0.8029 (ttm)
REVERT: A  957 MET cc_start: 0.9506 (mmm) cc_final: 0.9109 (mmm)
REVERT: A  966 TYR cc_start: 0.6171 (m-80) cc_final: 0.5944 (m-80)
REVERT: A 1060 MET cc_start: 0.7642 (ttp) cc_final: 0.7320 (tmm)
REVERT: A 1128 LEU cc_start: 0.8921 (mt) cc_final: 0.8649 (mt)
REVERT: A 1148 MET cc_start: 0.7471 (mtp) cc_final: 0.7206 (ptt)
REVERT: A 1153 ASP cc_start: 0.8912 (m-30) cc_final: 0.8687 (m-30)
REVERT: A 1169 VAL cc_start: 0.9465 (t) cc_final: 0.8933 (p)
REVERT: B  714 MET cc_start: 0.8405 (mpp) cc_final: 0.7914 (mpp)
REVERT: B  846 MET cc_start: 0.8357 (ttm) cc_final: 0.8037 (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: 0.9113 (mmm)
REVERT: B  966 TYR cc_start: 0.6394 (m-80) cc_final: 0.6092 (m-80)
REVERT: B 1060 MET cc_start: 0.7603 (ttp) cc_final: 0.7313 (tmm)
REVERT: B 1112 GLU cc_start: 0.9189 (mp0) cc_final: 0.8735 (mp0)
REVERT: B 1153 ASP cc_start: 0.8907 (m-30) cc_final: 0.8697 (m-30)
REVERT: B 1169 VAL cc_start: 0.9473 (t) cc_final: 0.9059 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.2087
  time to fit residues: 45.8036
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  : 0.954 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 52 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 60 optimal weight:    0.3980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.085906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.069133 restraints weight = 38419.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.071159 restraints weight = 25093.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.072569 restraints weight = 18287.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8286  Z= 0.169
  Angle     :  0.589   9.085  11204  Z= 0.315
  Chirality :  0.041   0.153   1200
  Planarity :  0.005   0.048   1432
  Dihedral  :  6.036  46.943   1104
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.61 %
    Favored  : 98.28 %
  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: -1.17 (0.27), residues: 980
  helix:  0.70 (0.24), residues: 436
  sheet: -1.86 (0.46), residues: 122
  loop : -2.04 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A1170 
 HIS   0.002   0.001   HIS A1092 
 PHE   0.014   0.001   PHE A 710 
 TYR   0.019   0.002   TYR A 769 
 ARG   0.003   0.000   ARG B1039 

*********************** 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
  144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 1.018 
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: 0.8383 (mpp) cc_final: 0.7884 (mpp)
REVERT: A  856 TRP cc_start: 0.4603 (p-90) cc_final: 0.4259 (p-90)
REVERT: A  957 MET cc_start: 0.9524 (mmm) cc_final: 0.9111 (mmm)
REVERT: A  966 TYR cc_start: 0.6225 (m-80) cc_final: 0.6021 (m-80)
REVERT: A 1023 ILE cc_start: 0.9105 (tt) cc_final: 0.8889 (tt)
REVERT: A 1060 MET cc_start: 0.7666 (ttp) cc_final: 0.7395 (tmm)
REVERT: A 1153 ASP cc_start: 0.8902 (m-30) cc_final: 0.8676 (m-30)
REVERT: A 1169 VAL cc_start: 0.9427 (t) cc_final: 0.9042 (p)
REVERT: B  714 MET cc_start: 0.8425 (mpp) cc_final: 0.7926 (mpp)
REVERT: B  957 MET cc_start: 0.9504 (mmm) cc_final: 0.9083 (mmm)
REVERT: B  966 TYR cc_start: 0.6428 (m-80) cc_final: 0.6135 (m-80)
REVERT: B 1023 ILE cc_start: 0.9048 (tt) cc_final: 0.8841 (tt)
REVERT: B 1060 MET cc_start: 0.7572 (ttp) cc_final: 0.7271 (tmm)
REVERT: B 1148 MET cc_start: 0.7152 (mtm) cc_final: 0.6943 (ttm)
REVERT: B 1153 ASP cc_start: 0.8904 (m-30) cc_final: 0.8701 (m-30)
REVERT: B 1169 VAL cc_start: 0.9455 (t) cc_final: 0.8997 (p)
REVERT: B 1173 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8965 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2335
  time to fit residues: 44.5901
Evaluate side-chains
  97 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 774 HIS
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1149 GLN
B 774 HIS
** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1149 GLN
B1192 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.080966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.064811 restraints weight = 39598.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.066813 restraints weight = 25037.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.068269 restraints weight = 17841.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8286  Z= 0.318
  Angle     :  0.712   9.585  11204  Z= 0.377
  Chirality :  0.045   0.155   1200
  Planarity :  0.006   0.044   1432
  Dihedral  :  6.385  50.010   1104
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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: -1.41 (0.27), residues: 980
  helix:  0.54 (0.24), residues: 446
  sheet: -1.85 (0.50), residues: 112
  loop : -2.34 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 820 
 HIS   0.005   0.001   HIS A1099 
 PHE   0.016   0.002   PHE B 750 
 TYR   0.022   0.002   TYR A 837 
 ARG   0.012   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
  125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  846 MET cc_start: 0.8502 (ttm) cc_final: 0.8093 (ttm)
REVERT: A  856 TRP cc_start: 0.4482 (p-90) cc_final: 0.4165 (p-90)
REVERT: A  957 MET cc_start: 0.9535 (mmm) cc_final: 0.9149 (mmm)
REVERT: A  966 TYR cc_start: 0.6104 (m-80) cc_final: 0.5883 (m-80)
REVERT: A 1102 ILE cc_start: 0.8964 (pt) cc_final: 0.8750 (pt)
REVERT: A 1153 ASP cc_start: 0.9015 (m-30) cc_final: 0.8792 (m-30)
REVERT: B  714 MET cc_start: 0.8341 (mpp) cc_final: 0.8097 (mpp)
REVERT: B  833 GLU cc_start: 0.8501 (pt0) cc_final: 0.8072 (pt0)
REVERT: B  846 MET cc_start: 0.8447 (ttm) cc_final: 0.8083 (ttm)
REVERT: B  885 LEU cc_start: 0.9404 (mt) cc_final: 0.9106 (mt)
REVERT: B  956 ARG cc_start: 0.9193 (mmt90) cc_final: 0.8987 (mmt90)
REVERT: B  957 MET cc_start: 0.9525 (mmm) cc_final: 0.9131 (mmm)
REVERT: B  966 TYR cc_start: 0.6299 (m-80) cc_final: 0.5996 (m-80)
REVERT: B 1148 MET cc_start: 0.7274 (mtm) cc_final: 0.7011 (ttm)
REVERT: B 1153 ASP cc_start: 0.9014 (m-30) cc_final: 0.8790 (m-30)
REVERT: B 1169 VAL cc_start: 0.9483 (t) cc_final: 0.8766 (t)
REVERT: B 1173 GLU cc_start: 0.9371 (mt-10) cc_final: 0.8993 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2118
  time to fit residues: 36.0302
Evaluate side-chains
  95 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 75 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 40 optimal weight:   10.0000
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.085108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.068432 restraints weight = 37150.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.070485 restraints weight = 24108.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.071887 restraints weight = 17431.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8286  Z= 0.155
  Angle     :  0.568   8.999  11204  Z= 0.303
  Chirality :  0.042   0.204   1200
  Planarity :  0.006   0.067   1432
  Dihedral  :  5.789  49.737   1104
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  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 : 0.64 %

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: -0.71 (0.27), residues: 980
  helix:  1.19 (0.24), residues: 446
  sheet: -1.81 (0.51), residues: 112
  loop : -1.96 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B1189 
 HIS   0.003   0.001   HIS B 909 
 PHE   0.014   0.001   PHE B 710 
 TYR   0.019   0.001   TYR A 769 
 ARG   0.007   0.001   ARG A1006 

*********************** 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
  132 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8310 (mpp) cc_final: 0.8023 (mpp)
REVERT: A  846 MET cc_start: 0.8386 (ttm) cc_final: 0.8034 (ttm)
REVERT: A  856 TRP cc_start: 0.4335 (p-90) cc_final: 0.4010 (p-90)
REVERT: A  957 MET cc_start: 0.9537 (mmm) cc_final: 0.9116 (mmm)
REVERT: A  966 TYR cc_start: 0.6183 (m-80) cc_final: 0.5972 (m-80)
REVERT: A 1038 TYR cc_start: 0.8780 (m-10) cc_final: 0.8564 (m-10)
REVERT: A 1132 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7822 (tp30)
REVERT: A 1153 ASP cc_start: 0.8989 (m-30) cc_final: 0.8768 (m-30)
REVERT: B  714 MET cc_start: 0.8332 (mpp) cc_final: 0.8068 (mpp)
REVERT: B  833 GLU cc_start: 0.8420 (pt0) cc_final: 0.8115 (pt0)
REVERT: B  846 MET cc_start: 0.8312 (ttm) cc_final: 0.8019 (ttm)
REVERT: B  885 LEU cc_start: 0.9245 (mt) cc_final: 0.9001 (mt)
REVERT: B  905 ASN cc_start: 0.8729 (m110) cc_final: 0.8482 (m-40)
REVERT: B  956 ARG cc_start: 0.9063 (mmt90) cc_final: 0.8776 (mmt90)
REVERT: B  957 MET cc_start: 0.9514 (mmm) cc_final: 0.9098 (mmm)
REVERT: B  966 TYR cc_start: 0.6356 (m-80) cc_final: 0.6057 (m-80)
REVERT: B 1128 LEU cc_start: 0.8875 (mt) cc_final: 0.8512 (mt)
REVERT: B 1148 MET cc_start: 0.7336 (mtm) cc_final: 0.7071 (mtp)
REVERT: B 1153 ASP cc_start: 0.8942 (m-30) cc_final: 0.8719 (m-30)
REVERT: B 1169 VAL cc_start: 0.9438 (t) cc_final: 0.8556 (t)
REVERT: B 1173 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8948 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1912
  time to fit residues: 35.0430
Evaluate side-chains
  94 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 79 optimal weight:   10.0000
   chunk 71 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.080468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.064686 restraints weight = 39487.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.066531 restraints weight = 25584.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.067796 restraints weight = 18545.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8286  Z= 0.343
  Angle     :  0.714   9.943  11204  Z= 0.379
  Chirality :  0.045   0.192   1200
  Planarity :  0.006   0.056   1432
  Dihedral  :  6.199  47.159   1104
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 16.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  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: -1.20 (0.27), residues: 980
  helix:  0.71 (0.24), residues: 456
  sheet: -1.58 (0.53), residues: 108
  loop : -2.35 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B 820 
 HIS   0.004   0.001   HIS B 753 
 PHE   0.016   0.002   PHE B 750 
 TYR   0.023   0.002   TYR B 837 
 ARG   0.007   0.001   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
  120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8409 (mpp) cc_final: 0.8102 (mpp)
REVERT: A  856 TRP cc_start: 0.4362 (p-90) cc_final: 0.3943 (p-90)
REVERT: A  882 LYS cc_start: 0.8935 (pttt) cc_final: 0.8544 (ptpp)
REVERT: A  956 ARG cc_start: 0.9206 (mmt90) cc_final: 0.8994 (mmt90)
REVERT: A  957 MET cc_start: 0.9543 (mmm) cc_final: 0.9126 (mmm)
REVERT: A  966 TYR cc_start: 0.6157 (m-80) cc_final: 0.5930 (m-80)
REVERT: A 1060 MET cc_start: 0.7963 (tmm) cc_final: 0.7461 (tmm)
REVERT: A 1153 ASP cc_start: 0.9054 (m-30) cc_final: 0.8846 (m-30)
REVERT: B  714 MET cc_start: 0.8417 (mpp) cc_final: 0.8119 (mpp)
REVERT: B  833 GLU cc_start: 0.8476 (pt0) cc_final: 0.8165 (pt0)
REVERT: B  885 LEU cc_start: 0.9298 (mt) cc_final: 0.9093 (mt)
REVERT: B  905 ASN cc_start: 0.8817 (m110) cc_final: 0.8403 (m110)
REVERT: B  917 TYR cc_start: 0.8999 (m-10) cc_final: 0.8793 (m-80)
REVERT: B  957 MET cc_start: 0.9531 (mmm) cc_final: 0.9101 (mmm)
REVERT: B  966 TYR cc_start: 0.6261 (m-80) cc_final: 0.5946 (m-80)
REVERT: B 1060 MET cc_start: 0.7954 (tmm) cc_final: 0.7560 (tmm)
REVERT: B 1148 MET cc_start: 0.7315 (mtm) cc_final: 0.6986 (ttm)
REVERT: B 1153 ASP cc_start: 0.9009 (m-30) cc_final: 0.8780 (m-30)
REVERT: B 1169 VAL cc_start: 0.9522 (t) cc_final: 0.8734 (t)
REVERT: B 1173 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8949 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1728
  time to fit residues: 29.8990
Evaluate side-chains
  90 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 93 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 71 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0670
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6718

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.085175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.068455 restraints weight = 37599.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.070465 restraints weight = 24355.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.071930 restraints weight = 17667.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.4256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8286  Z= 0.153
  Angle     :  0.573  11.381  11204  Z= 0.303
  Chirality :  0.042   0.227   1200
  Planarity :  0.005   0.045   1432
  Dihedral  :  5.593  38.899   1104
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  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: -0.50 (0.28), residues: 980
  helix:  1.36 (0.24), residues: 456
  sheet: -1.61 (0.50), residues: 122
  loop : -1.95 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B1012 
 PHE   0.014   0.001   PHE B 741 
 TYR   0.020   0.001   TYR A 769 
 ARG   0.004   0.000   ARG A1131 

*********************** 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
  128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8909 (p0) cc_final: 0.6797 (p0)
REVERT: A  714 MET cc_start: 0.8294 (mpp) cc_final: 0.7839 (mpp)
REVERT: A  741 PHE cc_start: 0.8187 (t80) cc_final: 0.7976 (t80)
REVERT: A  818 ASP cc_start: 0.7898 (m-30) cc_final: 0.7566 (m-30)
REVERT: A  833 GLU cc_start: 0.8467 (pt0) cc_final: 0.8137 (pt0)
REVERT: A  846 MET cc_start: 0.8366 (ttm) cc_final: 0.8014 (ttm)
REVERT: A  856 TRP cc_start: 0.4333 (p-90) cc_final: 0.3990 (p-90)
REVERT: A  905 ASN cc_start: 0.8778 (m-40) cc_final: 0.8390 (m-40)
REVERT: A  957 MET cc_start: 0.9535 (mmm) cc_final: 0.9103 (mmm)
REVERT: A  966 TYR cc_start: 0.6096 (m-80) cc_final: 0.5893 (m-80)
REVERT: A 1023 ILE cc_start: 0.9136 (tt) cc_final: 0.8887 (tt)
REVERT: A 1144 LYS cc_start: 0.8543 (tttt) cc_final: 0.8326 (tptp)
REVERT: A 1153 ASP cc_start: 0.8986 (m-30) cc_final: 0.8783 (m-30)
REVERT: B  714 MET cc_start: 0.8283 (mpp) cc_final: 0.8016 (mpp)
REVERT: B  818 ASP cc_start: 0.8287 (m-30) cc_final: 0.8066 (m-30)
REVERT: B  833 GLU cc_start: 0.8454 (pt0) cc_final: 0.8095 (tt0)
REVERT: B  846 MET cc_start: 0.8356 (ttm) cc_final: 0.8027 (ttm)
REVERT: B  905 ASN cc_start: 0.8747 (m110) cc_final: 0.8496 (m-40)
REVERT: B  917 TYR cc_start: 0.8888 (m-10) cc_final: 0.8662 (m-80)
REVERT: B  957 MET cc_start: 0.9515 (mmm) cc_final: 0.9064 (mmm)
REVERT: B  966 TYR cc_start: 0.6261 (m-80) cc_final: 0.5963 (m-80)
REVERT: B 1060 MET cc_start: 0.7937 (tmm) cc_final: 0.7637 (tmm)
REVERT: B 1148 MET cc_start: 0.7255 (mtm) cc_final: 0.6975 (mtp)
REVERT: B 1153 ASP cc_start: 0.8954 (m-30) cc_final: 0.8725 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1570
  time to fit residues: 30.0101
Evaluate side-chains
  95 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 78 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0030
   chunk 45 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6592

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.086247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.069070 restraints weight = 37571.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.071253 restraints weight = 23758.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.072850 restraints weight = 16975.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8286  Z= 0.153
  Angle     :  0.575  11.175  11204  Z= 0.302
  Chirality :  0.042   0.237   1200
  Planarity :  0.005   0.038   1432
  Dihedral  :  5.379  47.177   1104
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  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: -0.19 (0.28), residues: 980
  helix:  1.62 (0.24), residues: 458
  sheet: -1.44 (0.51), residues: 122
  loop : -1.83 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 856 
 HIS   0.003   0.001   HIS A 883 
 PHE   0.024   0.001   PHE A 710 
 TYR   0.014   0.001   TYR A 920 
 ARG   0.003   0.000   ARG B 734 

*********************** 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
  129 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.9028 (p0) cc_final: 0.6769 (p0)
REVERT: A  714 MET cc_start: 0.8213 (mpp) cc_final: 0.7766 (mpp)
REVERT: A  833 GLU cc_start: 0.8429 (pt0) cc_final: 0.8192 (pt0)
REVERT: A  846 MET cc_start: 0.8347 (ttm) cc_final: 0.8008 (ttm)
REVERT: A  856 TRP cc_start: 0.4173 (p-90) cc_final: 0.3743 (p-90)
REVERT: A  905 ASN cc_start: 0.8791 (m-40) cc_final: 0.8376 (m-40)
REVERT: A  917 TYR cc_start: 0.9056 (m-10) cc_final: 0.8786 (m-80)
REVERT: A  957 MET cc_start: 0.9534 (mmm) cc_final: 0.9084 (mmm)
REVERT: A  966 TYR cc_start: 0.6144 (m-80) cc_final: 0.5944 (m-80)
REVERT: A 1038 TYR cc_start: 0.8819 (m-80) cc_final: 0.8550 (m-10)
REVERT: A 1125 ILE cc_start: 0.8887 (mt) cc_final: 0.8586 (tp)
REVERT: A 1128 LEU cc_start: 0.8602 (mm) cc_final: 0.8208 (mm)
REVERT: A 1144 LYS cc_start: 0.8565 (tttt) cc_final: 0.8354 (tmtt)
REVERT: B  712 ASP cc_start: 0.8970 (p0) cc_final: 0.6800 (p0)
REVERT: B  714 MET cc_start: 0.8238 (mpp) cc_final: 0.7868 (mpp)
REVERT: B  817 GLU cc_start: 0.9058 (pm20) cc_final: 0.8844 (pm20)
REVERT: B  833 GLU cc_start: 0.8396 (pt0) cc_final: 0.8068 (tt0)
REVERT: B  846 MET cc_start: 0.8352 (ttm) cc_final: 0.8030 (ttm)
REVERT: B  905 ASN cc_start: 0.8793 (m110) cc_final: 0.8506 (m-40)
REVERT: B  917 TYR cc_start: 0.8881 (m-10) cc_final: 0.8610 (m-80)
REVERT: B  957 MET cc_start: 0.9504 (mmm) cc_final: 0.9036 (mmm)
REVERT: B 1148 MET cc_start: 0.7301 (mtm) cc_final: 0.7058 (mtp)
REVERT: B 1153 ASP cc_start: 0.8993 (m-30) cc_final: 0.8766 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1513
  time to fit residues: 29.0681
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  : 0.855 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 53 optimal weight:    8.9990
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    8.9990
   chunk 85 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0000
   chunk 68 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 79 optimal weight:   10.0000
   overall best weight:    0.9788

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.085847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.068683 restraints weight = 38114.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.070686 restraints weight = 24973.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.072220 restraints weight = 18266.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.4767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8286  Z= 0.156
  Angle     :  0.568  10.762  11204  Z= 0.296
  Chirality :  0.042   0.222   1200
  Planarity :  0.004   0.038   1432
  Dihedral  :  5.312  44.788   1104
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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: -0.08 (0.28), residues: 980
  helix:  1.70 (0.24), residues: 460
  sheet: -1.18 (0.52), residues: 118
  loop : -1.86 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B1189 
 HIS   0.014   0.001   HIS A1099 
 PHE   0.018   0.001   PHE A 710 
 TYR   0.023   0.001   TYR A 769 
 ARG   0.003   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
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.9011 (p0) cc_final: 0.6785 (p0)
REVERT: A  714 MET cc_start: 0.8223 (mpp) cc_final: 0.7752 (mpp)
REVERT: A  833 GLU cc_start: 0.8429 (pt0) cc_final: 0.8193 (pt0)
REVERT: A  846 MET cc_start: 0.8320 (ttm) cc_final: 0.8026 (ttm)
REVERT: A  856 TRP cc_start: 0.4069 (p-90) cc_final: 0.3550 (p-90)
REVERT: A  882 LYS cc_start: 0.8823 (pttt) cc_final: 0.8475 (ptpp)
REVERT: A  905 ASN cc_start: 0.8757 (m-40) cc_final: 0.8378 (m-40)
REVERT: A  957 MET cc_start: 0.9533 (mmm) cc_final: 0.9089 (mmm)
REVERT: A 1038 TYR cc_start: 0.8825 (m-80) cc_final: 0.8531 (m-80)
REVERT: A 1125 ILE cc_start: 0.8820 (mt) cc_final: 0.8459 (tp)
REVERT: B  712 ASP cc_start: 0.9020 (p0) cc_final: 0.6338 (p0)
REVERT: B  714 MET cc_start: 0.8239 (mpp) cc_final: 0.7746 (mpp)
REVERT: B  833 GLU cc_start: 0.8354 (pt0) cc_final: 0.8070 (tt0)
REVERT: B  846 MET cc_start: 0.8338 (ttm) cc_final: 0.8034 (ttm)
REVERT: B  856 TRP cc_start: 0.3689 (p-90) cc_final: 0.2666 (p-90)
REVERT: B  885 LEU cc_start: 0.9354 (mt) cc_final: 0.9112 (mt)
REVERT: B  905 ASN cc_start: 0.8820 (m110) cc_final: 0.8539 (m-40)
REVERT: B  917 TYR cc_start: 0.8838 (m-10) cc_final: 0.8593 (m-80)
REVERT: B  957 MET cc_start: 0.9514 (mmm) cc_final: 0.9035 (mmm)
REVERT: B  966 TYR cc_start: 0.5432 (m-80) cc_final: 0.5163 (m-80)
REVERT: B 1038 TYR cc_start: 0.8704 (m-10) cc_final: 0.8461 (m-10)
REVERT: B 1148 MET cc_start: 0.7330 (mtm) cc_final: 0.7078 (mtp)
REVERT: B 1153 ASP cc_start: 0.8978 (m-30) cc_final: 0.8772 (m-30)
REVERT: B 1169 VAL cc_start: 0.9473 (t) cc_final: 0.8642 (t)
REVERT: B 1173 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8947 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1532
  time to fit residues: 29.0742
Evaluate side-chains
  94 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 88 optimal weight:    0.1980
   chunk 1 optimal weight:    7.9990
   chunk 62 optimal weight:    3.9990
   chunk 86 optimal weight:    8.9990
   chunk 19 optimal weight:   20.0000
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.085336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.068430 restraints weight = 38227.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.070444 restraints weight = 24815.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.072012 restraints weight = 18014.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4842

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= 0.170
  Angle     :  0.558   9.395  11204  Z= 0.293
  Chirality :  0.042   0.192   1200
  Planarity :  0.004   0.037   1432
  Dihedral  :  5.255  45.034   1104
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  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: -0.04 (0.28), residues: 980
  helix:  1.77 (0.24), residues: 460
  sheet: -1.12 (0.52), residues: 118
  loop : -1.89 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B1189 
 HIS   0.012   0.001   HIS A1099 
 PHE   0.017   0.001   PHE A 710 
 TYR   0.012   0.001   TYR A 848 
 ARG   0.004   0.000   ARG A1039 

********************** 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
  125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.9025 (p0) cc_final: 0.6998 (p0)
REVERT: A  714 MET cc_start: 0.8273 (mpp) cc_final: 0.7818 (mpp)
REVERT: A  856 TRP cc_start: 0.3951 (p-90) cc_final: 0.3336 (p-90)
REVERT: A  882 LYS cc_start: 0.8821 (pttt) cc_final: 0.8435 (ptpp)
REVERT: A  905 ASN cc_start: 0.8779 (m-40) cc_final: 0.8411 (m-40)
REVERT: A  917 TYR cc_start: 0.8993 (m-10) cc_final: 0.8788 (m-80)
REVERT: A  957 MET cc_start: 0.9529 (mmm) cc_final: 0.9056 (mmm)
REVERT: A  966 TYR cc_start: 0.6355 (m-10) cc_final: 0.6100 (m-80)
REVERT: A 1023 ILE cc_start: 0.8851 (mm) cc_final: 0.8572 (tt)
REVERT: A 1038 TYR cc_start: 0.8812 (m-80) cc_final: 0.8534 (m-80)
REVERT: A 1125 ILE cc_start: 0.8823 (mt) cc_final: 0.8454 (tp)
REVERT: B  712 ASP cc_start: 0.9029 (p0) cc_final: 0.8238 (p0)
REVERT: B  817 GLU cc_start: 0.8400 (pm20) cc_final: 0.8148 (pt0)
REVERT: B  833 GLU cc_start: 0.8335 (pt0) cc_final: 0.8063 (tt0)
REVERT: B  846 MET cc_start: 0.8358 (ttm) cc_final: 0.8031 (ttm)
REVERT: B  856 TRP cc_start: 0.3782 (p-90) cc_final: 0.2785 (p-90)
REVERT: B  885 LEU cc_start: 0.9352 (mt) cc_final: 0.9039 (mt)
REVERT: B  905 ASN cc_start: 0.8808 (m110) cc_final: 0.8520 (m-40)
REVERT: B  917 TYR cc_start: 0.8871 (m-10) cc_final: 0.8584 (m-80)
REVERT: B  957 MET cc_start: 0.9514 (mmm) cc_final: 0.9047 (mmm)
REVERT: B  966 TYR cc_start: 0.5506 (m-80) cc_final: 0.5233 (m-80)
REVERT: B 1038 TYR cc_start: 0.8710 (m-10) cc_final: 0.8465 (m-10)
REVERT: B 1148 MET cc_start: 0.7377 (mtm) cc_final: 0.7094 (mtp)
REVERT: B 1153 ASP cc_start: 0.8978 (m-30) cc_final: 0.8763 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1517
  time to fit residues: 28.6126
Evaluate side-chains
  90 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0040
   chunk 39 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7392

-------------------------------------------------------------------------------
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**
B 753 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 = 0.4011 r_free = 0.4011 target = 0.086647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.069376 restraints weight = 37737.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.071466 restraints weight = 24608.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.072913 restraints weight = 17893.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.5036

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= 0.149
  Angle     :  0.547   9.950  11204  Z= 0.283
  Chirality :  0.041   0.181   1200
  Planarity :  0.004   0.039   1432
  Dihedral  :  5.115  44.617   1104
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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:  0.18 (0.29), residues: 980
  helix:  1.98 (0.24), residues: 460
  sheet: -1.07 (0.52), residues: 118
  loop : -1.81 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1189 
 HIS   0.010   0.001   HIS A1099 
 PHE   0.016   0.001   PHE A 710 
 TYR   0.020   0.001   TYR A 769 
 ARG   0.003   0.000   ARG B 734 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2886.24 seconds
wall clock time: 53 minutes 1.28 seconds (3181.28 seconds total)