Starting phenix.real_space_refine
on Fri Aug 22 21:51:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kgl_37225/08_2025/8kgl_37225.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kgl_37225/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kgl_37225/08_2025/8kgl_37225.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kgl_37225/08_2025/8kgl_37225.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kgl_37225/08_2025/8kgl_37225.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kgl_37225/08_2025/8kgl_37225.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.99, per 1000 atoms: 0.25
  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: 0.54
  Conformation dependent library (CDL) restraints added in 508.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  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: 0.27
  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: 1.23

  Time building geometry restraints manager: 0.74 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: 0.02
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:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.000
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.080
-------------------------------------------------------------------------------
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= 0.336
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG B 940 
 TYR   0.032   0.003   TYR B 917 
 PHE   0.024   0.003   PHE B 750 
 TRP   0.084   0.007   TRP B1170 
 HIS   0.007   0.002   HIS B 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.00707 ( 8286)
  covalent geometry    : angle       1.06410 (11204)
  hydrogen bonds       : bond        0.13736 (  382)
  hydrogen bonds       : angle       6.00281 ( 1077)

*********************** 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  : 0.281 
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: 0.1151
  time to fit residues: 30.3396
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  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.0784

-------------------------------------------------------------------------------
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**
B1099 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.083571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.067265 restraints weight = 38570.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.069307 restraints weight = 24551.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.070692 restraints weight = 17626.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.071602 restraints weight = 13820.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.072448 restraints weight = 11621.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8286  Z= 0.158
  Angle     :  0.665   9.478  11204  Z= 0.357
  Chirality :  0.043   0.151   1200
  Planarity :  0.007   0.051   1432
  Dihedral  :  6.844  47.421   1104
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  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 : 0.85 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.92 (0.26), residues: 980
  helix: -0.01 (0.24), residues: 430
  sheet: -2.22 (0.48), residues: 112
  loop : -2.32 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 716 
 TYR   0.016   0.002   TYR B 917 
 PHE   0.012   0.002   PHE B 750 
 TRP   0.039   0.003   TRP A1170 
 HIS   0.005   0.001   HIS B1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8286)
  covalent geometry    : angle       0.66543 (11204)
  hydrogen bonds       : bond        0.04867 (  382)
  hydrogen bonds       : angle       4.73550 ( 1077)

*********************** 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
  153 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.278 
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  711 LEU cc_start: 0.9393 (mt) cc_final: 0.8946 (tp)
REVERT: A  714 MET cc_start: 0.8355 (mpp) cc_final: 0.7868 (mpp)
REVERT: A  846 MET cc_start: 0.8388 (ttm) cc_final: 0.8039 (ttm)
REVERT: A  957 MET cc_start: 0.9528 (mmm) cc_final: 0.9113 (mmm)
REVERT: A  966 TYR cc_start: 0.6263 (m-80) cc_final: 0.6018 (m-80)
REVERT: A 1060 MET cc_start: 0.7670 (ttp) cc_final: 0.7246 (tmm)
REVERT: A 1148 MET cc_start: 0.7552 (mtp) cc_final: 0.7219 (ptt)
REVERT: A 1153 ASP cc_start: 0.8850 (m-30) cc_final: 0.8628 (m-30)
REVERT: A 1169 VAL cc_start: 0.9492 (t) cc_final: 0.8645 (t)
REVERT: B  714 MET cc_start: 0.8384 (mpp) cc_final: 0.7908 (mpp)
REVERT: B  846 MET cc_start: 0.8338 (ttm) cc_final: 0.8013 (ttm)
REVERT: B  957 MET cc_start: 0.9523 (mmm) cc_final: 0.9109 (mmm)
REVERT: B  966 TYR cc_start: 0.6470 (m-80) cc_final: 0.6158 (m-80)
REVERT: B 1060 MET cc_start: 0.7639 (ttp) cc_final: 0.7241 (tmm)
REVERT: B 1148 MET cc_start: 0.7248 (mtm) cc_final: 0.7010 (ttm)
REVERT: B 1153 ASP cc_start: 0.8857 (m-30) cc_final: 0.8636 (m-30)
REVERT: B 1169 VAL cc_start: 0.9504 (t) cc_final: 0.9214 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0875
  time to fit residues: 18.1409
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  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 64 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0170
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 92 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 59 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.1622

-------------------------------------------------------------------------------
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
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.086337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.069014 restraints weight = 38060.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.071145 restraints weight = 24280.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.072677 restraints weight = 17472.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.073762 restraints weight = 13592.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.074646 restraints weight = 11264.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3126

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= 0.126
  Angle     :  0.584   8.712  11204  Z= 0.313
  Chirality :  0.041   0.150   1200
  Planarity :  0.005   0.048   1432
  Dihedral  :  6.064  48.416   1104
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.27), residues: 980
  helix:  0.72 (0.24), residues: 434
  sheet: -1.89 (0.46), residues: 122
  loop : -2.08 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1039 
 TYR   0.018   0.002   TYR B 769 
 PHE   0.011   0.001   PHE B 710 
 TRP   0.015   0.002   TRP A1170 
 HIS   0.002   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 8286)
  covalent geometry    : angle       0.58417 (11204)
  hydrogen bonds       : bond        0.04323 (  382)
  hydrogen bonds       : angle       4.30504 ( 1077)

*********************** 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
  152 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.314 
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: 0.8390 (mpp) cc_final: 0.7926 (mpp)
REVERT: A  814 PHE cc_start: 0.8410 (m-80) cc_final: 0.8206 (m-10)
REVERT: A  957 MET cc_start: 0.9527 (mmm) cc_final: 0.9103 (mmm)
REVERT: A  966 TYR cc_start: 0.6123 (m-80) cc_final: 0.5904 (m-80)
REVERT: A 1060 MET cc_start: 0.7611 (ttp) cc_final: 0.7342 (tmm)
REVERT: A 1153 ASP cc_start: 0.8911 (m-30) cc_final: 0.8666 (m-30)
REVERT: B  714 MET cc_start: 0.8399 (mpp) cc_final: 0.7947 (mpp)
REVERT: B  905 ASN cc_start: 0.8717 (m110) cc_final: 0.8459 (m-40)
REVERT: B  957 MET cc_start: 0.9515 (mmm) cc_final: 0.9075 (mmm)
REVERT: B  966 TYR cc_start: 0.6367 (m-80) cc_final: 0.6096 (m-80)
REVERT: B 1060 MET cc_start: 0.7552 (ttp) cc_final: 0.7287 (tmm)
REVERT: B 1112 GLU cc_start: 0.9197 (mp0) cc_final: 0.8764 (mp0)
REVERT: B 1148 MET cc_start: 0.7173 (mtm) cc_final: 0.6959 (mtp)
REVERT: B 1153 ASP cc_start: 0.8896 (m-30) cc_final: 0.8689 (m-30)
REVERT: B 1169 VAL cc_start: 0.9476 (t) cc_final: 0.8749 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.1028
  time to fit residues: 20.6143
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  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 94 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 72 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   overall best weight:    4.1986

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.081651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.065387 restraints weight = 41153.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.067265 restraints weight = 26668.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.068566 restraints weight = 19376.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.069594 restraints weight = 15345.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.070273 restraints weight = 12765.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8286  Z= 0.239
  Angle     :  0.721  10.178  11204  Z= 0.382
  Chirality :  0.045   0.186   1200
  Planarity :  0.006   0.047   1432
  Dihedral  :  6.358  51.923   1104
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.78 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.40 (0.26), residues: 980
  helix:  0.54 (0.23), residues: 448
  sheet: -1.63 (0.51), residues: 108
  loop : -2.40 (0.29), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1039 
 TYR   0.029   0.002   TYR A 837 
 PHE   0.017   0.002   PHE B 750 
 TRP   0.020   0.003   TRP B 820 
 HIS   0.005   0.001   HIS B 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8286)
  covalent geometry    : angle       0.72149 (11204)
  hydrogen bonds       : bond        0.04593 (  382)
  hydrogen bonds       : angle       4.62495 ( 1077)

*********************** 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  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8410 (mpp) cc_final: 0.8124 (mpp)
REVERT: A  846 MET cc_start: 0.8437 (ttm) cc_final: 0.8050 (ttm)
REVERT: A  957 MET cc_start: 0.9545 (mmm) cc_final: 0.9135 (mmm)
REVERT: A  966 TYR cc_start: 0.6127 (m-80) cc_final: 0.5734 (m-80)
REVERT: A 1038 TYR cc_start: 0.8885 (m-10) cc_final: 0.8643 (m-10)
REVERT: A 1102 ILE cc_start: 0.8968 (pt) cc_final: 0.8766 (pt)
REVERT: A 1132 GLU cc_start: 0.7961 (tp30) cc_final: 0.7714 (tp30)
REVERT: A 1153 ASP cc_start: 0.8920 (m-30) cc_final: 0.8703 (m-30)
REVERT: A 1169 VAL cc_start: 0.9377 (t) cc_final: 0.9054 (t)
REVERT: A 1173 GLU cc_start: 0.8882 (mp0) cc_final: 0.8303 (mp0)
REVERT: B  714 MET cc_start: 0.8341 (mpp) cc_final: 0.8083 (mpp)
REVERT: B  833 GLU cc_start: 0.8459 (pt0) cc_final: 0.8094 (pt0)
REVERT: B  846 MET cc_start: 0.8405 (ttm) cc_final: 0.8052 (ttm)
REVERT: B  885 LEU cc_start: 0.9373 (mt) cc_final: 0.9093 (mt)
REVERT: B  957 MET cc_start: 0.9526 (mmm) cc_final: 0.9107 (mmm)
REVERT: B  966 TYR cc_start: 0.6309 (m-80) cc_final: 0.6009 (m-80)
REVERT: B 1148 MET cc_start: 0.7345 (mtm) cc_final: 0.7073 (ttm)
REVERT: B 1153 ASP cc_start: 0.8915 (m-30) cc_final: 0.8695 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0944
  time to fit residues: 16.2438
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  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    0.0570
   chunk 70 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    2.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.083428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.066701 restraints weight = 38876.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.068769 restraints weight = 24316.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.070303 restraints weight = 17289.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.071332 restraints weight = 13331.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.072178 restraints weight = 10979.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8286  Z= 0.144
  Angle     :  0.607   9.387  11204  Z= 0.322
  Chirality :  0.043   0.218   1200
  Planarity :  0.006   0.071   1432
  Dihedral  :  5.940  49.485   1104
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 12.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  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 : 0.75 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.03 (0.27), residues: 980
  helix:  0.92 (0.24), residues: 458
  sheet: -1.86 (0.51), residues: 112
  loop : -2.24 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1039 
 TYR   0.022   0.002   TYR A 769 
 PHE   0.012   0.001   PHE B 710 
 TRP   0.015   0.002   TRP B1189 
 HIS   0.002   0.001   HIS A1010 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8286)
  covalent geometry    : angle       0.60733 (11204)
  hydrogen bonds       : bond        0.04219 (  382)
  hydrogen bonds       : angle       4.23380 ( 1077)

*********************** 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
  124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  714 MET cc_start: 0.8365 (mpp) cc_final: 0.8084 (mpp)
REVERT: A  846 MET cc_start: 0.8349 (ttm) cc_final: 0.7975 (ttm)
REVERT: A  856 TRP cc_start: 0.3941 (p-90) cc_final: 0.2582 (p-90)
REVERT: A  905 ASN cc_start: 0.8735 (m110) cc_final: 0.8295 (m110)
REVERT: A  957 MET cc_start: 0.9543 (mmm) cc_final: 0.9139 (mmm)
REVERT: A  966 TYR cc_start: 0.6130 (m-80) cc_final: 0.5752 (m-80)
REVERT: A 1023 ILE cc_start: 0.9066 (tt) cc_final: 0.8823 (tt)
REVERT: A 1153 ASP cc_start: 0.8983 (m-30) cc_final: 0.8751 (m-30)
REVERT: B  714 MET cc_start: 0.8374 (mpp) cc_final: 0.8106 (mpp)
REVERT: B  833 GLU cc_start: 0.8371 (pt0) cc_final: 0.8006 (pt0)
REVERT: B  846 MET cc_start: 0.8357 (ttm) cc_final: 0.7982 (ttm)
REVERT: B  856 TRP cc_start: 0.4049 (p-90) cc_final: 0.3302 (p-90)
REVERT: B  885 LEU cc_start: 0.9288 (mt) cc_final: 0.9077 (mt)
REVERT: B  905 ASN cc_start: 0.8746 (m110) cc_final: 0.8458 (m-40)
REVERT: B  957 MET cc_start: 0.9522 (mmm) cc_final: 0.9107 (mmm)
REVERT: B  966 TYR cc_start: 0.6368 (m-80) cc_final: 0.6070 (m-80)
REVERT: B 1148 MET cc_start: 0.7303 (mtm) cc_final: 0.7032 (mtp)
REVERT: B 1153 ASP cc_start: 0.8937 (m-30) cc_final: 0.8710 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0786
  time to fit residues: 14.0844
Evaluate side-chains
  92 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 87 optimal weight:    0.0000
   chunk 96 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 23 optimal weight:   30.0000
   chunk 30 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0040
   chunk 47 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    0.6000

-------------------------------------------------------------------------------
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
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.086378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.069459 restraints weight = 37363.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.071458 restraints weight = 24083.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.072995 restraints weight = 17505.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.074076 restraints weight = 13638.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.074856 restraints weight = 11235.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8286  Z= 0.108
  Angle     :  0.545   9.109  11204  Z= 0.289
  Chirality :  0.041   0.147   1200
  Planarity :  0.005   0.051   1432
  Dihedral  :  5.424  40.637   1104
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  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 : 0.53 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.28), residues: 980
  helix:  1.44 (0.24), residues: 458
  sheet: -1.62 (0.49), residues: 122
  loop : -1.99 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 799 
 TYR   0.010   0.001   TYR A1043 
 PHE   0.012   0.001   PHE B 710 
 TRP   0.012   0.001   TRP B1189 
 HIS   0.002   0.001   HIS B1012 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 8286)
  covalent geometry    : angle       0.54457 (11204)
  hydrogen bonds       : bond        0.03784 (  382)
  hydrogen bonds       : angle       3.95390 ( 1077)

*********************** 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
  138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8932 (p0) cc_final: 0.6704 (p0)
REVERT: A  714 MET cc_start: 0.8250 (mpp) cc_final: 0.7811 (mpp)
REVERT: A  814 PHE cc_start: 0.8220 (m-80) cc_final: 0.7952 (m-80)
REVERT: A  833 GLU cc_start: 0.8485 (pt0) cc_final: 0.8134 (pt0)
REVERT: A  856 TRP cc_start: 0.3706 (p-90) cc_final: 0.2715 (p-90)
REVERT: A  882 LYS cc_start: 0.8805 (pttt) cc_final: 0.8435 (ptpp)
REVERT: A  905 ASN cc_start: 0.8797 (m110) cc_final: 0.8362 (m110)
REVERT: A  917 TYR cc_start: 0.8952 (m-10) cc_final: 0.8711 (m-80)
REVERT: A  957 MET cc_start: 0.9528 (mmm) cc_final: 0.9081 (mmm)
REVERT: A 1060 MET cc_start: 0.7900 (tmm) cc_final: 0.7514 (tmm)
REVERT: A 1112 GLU cc_start: 0.9289 (mp0) cc_final: 0.9086 (mp0)
REVERT: A 1153 ASP cc_start: 0.8946 (m-30) cc_final: 0.8744 (m-30)
REVERT: B  712 ASP cc_start: 0.8908 (p0) cc_final: 0.6717 (p0)
REVERT: B  714 MET cc_start: 0.8243 (mpp) cc_final: 0.7826 (mpp)
REVERT: B  833 GLU cc_start: 0.8340 (pt0) cc_final: 0.8038 (pt0)
REVERT: B  856 TRP cc_start: 0.3971 (p-90) cc_final: 0.3330 (p-90)
REVERT: B  905 ASN cc_start: 0.8737 (m110) cc_final: 0.8454 (m-40)
REVERT: B  917 TYR cc_start: 0.8857 (m-10) cc_final: 0.8541 (m-80)
REVERT: B  956 ARG cc_start: 0.9083 (mmt90) cc_final: 0.8806 (mmt90)
REVERT: B  957 MET cc_start: 0.9502 (mmm) cc_final: 0.9045 (mmm)
REVERT: B  966 TYR cc_start: 0.6318 (m-80) cc_final: 0.6035 (m-80)
REVERT: B  990 PHE cc_start: 0.8551 (m-10) cc_final: 0.8245 (m-10)
REVERT: B 1038 TYR cc_start: 0.8658 (m-10) cc_final: 0.8415 (m-10)
REVERT: B 1060 MET cc_start: 0.7897 (tmm) cc_final: 0.7503 (tmm)
REVERT: B 1112 GLU cc_start: 0.9262 (mp0) cc_final: 0.9057 (mp0)
REVERT: B 1148 MET cc_start: 0.7299 (mtm) cc_final: 0.7037 (mtp)
REVERT: B 1153 ASP cc_start: 0.8896 (m-30) cc_final: 0.8680 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0787
  time to fit residues: 15.6172
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  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    9.9990
   chunk 78 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    6.9990
   chunk 82 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 64 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    2.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.084208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.067740 restraints weight = 39424.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.069689 restraints weight = 25234.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.071079 restraints weight = 18168.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.072135 restraints weight = 14254.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.072811 restraints weight = 11771.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.4323

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= 0.148
  Angle     :  0.586   9.581  11204  Z= 0.312
  Chirality :  0.043   0.180   1200
  Planarity :  0.005   0.041   1432
  Dihedral  :  5.467  41.333   1104
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.28), residues: 980
  helix:  1.48 (0.24), residues: 458
  sheet: -1.62 (0.49), residues: 122
  loop : -2.03 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1039 
 TYR   0.026   0.002   TYR A 769 
 PHE   0.014   0.001   PHE B 741 
 TRP   0.016   0.002   TRP B1189 
 HIS   0.003   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8286)
  covalent geometry    : angle       0.58572 (11204)
  hydrogen bonds       : bond        0.03894 (  382)
  hydrogen bonds       : angle       4.09941 ( 1077)

*********************** 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
  121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8905 (p0) cc_final: 0.6715 (p0)
REVERT: A  714 MET cc_start: 0.8313 (mpp) cc_final: 0.7844 (mpp)
REVERT: A  833 GLU cc_start: 0.8526 (pt0) cc_final: 0.8201 (pt0)
REVERT: A  846 MET cc_start: 0.8298 (ttp) cc_final: 0.8043 (ttm)
REVERT: A  856 TRP cc_start: 0.3717 (p-90) cc_final: 0.2532 (p-90)
REVERT: A  882 LYS cc_start: 0.8877 (pttt) cc_final: 0.8483 (ptpp)
REVERT: A  905 ASN cc_start: 0.8763 (m110) cc_final: 0.8443 (m-40)
REVERT: A  917 TYR cc_start: 0.9035 (m-10) cc_final: 0.8826 (m-80)
REVERT: A  957 MET cc_start: 0.9531 (mmm) cc_final: 0.9108 (mmm)
REVERT: A 1038 TYR cc_start: 0.8826 (m-80) cc_final: 0.8535 (m-10)
REVERT: A 1112 GLU cc_start: 0.9285 (mp0) cc_final: 0.9032 (mp0)
REVERT: A 1153 ASP cc_start: 0.8956 (m-30) cc_final: 0.8742 (m-30)
REVERT: B  712 ASP cc_start: 0.8863 (p0) cc_final: 0.6732 (p0)
REVERT: B  714 MET cc_start: 0.8341 (mpp) cc_final: 0.7907 (mpp)
REVERT: B  833 GLU cc_start: 0.8339 (pt0) cc_final: 0.8043 (tt0)
REVERT: B  856 TRP cc_start: 0.3936 (p-90) cc_final: 0.3231 (p-90)
REVERT: B  905 ASN cc_start: 0.8769 (m110) cc_final: 0.8490 (m-40)
REVERT: B  956 ARG cc_start: 0.9128 (mmt90) cc_final: 0.8866 (mmt90)
REVERT: B  957 MET cc_start: 0.9499 (mmm) cc_final: 0.9047 (mmm)
REVERT: B  990 PHE cc_start: 0.8551 (m-10) cc_final: 0.8221 (m-10)
REVERT: B 1038 TYR cc_start: 0.8691 (m-10) cc_final: 0.8467 (m-10)
REVERT: B 1060 MET cc_start: 0.7921 (tmm) cc_final: 0.7607 (tmm)
REVERT: B 1112 GLU cc_start: 0.9289 (mp0) cc_final: 0.9007 (mp0)
REVERT: B 1148 MET cc_start: 0.7315 (mtm) cc_final: 0.7054 (mtp)
REVERT: B 1153 ASP cc_start: 0.8900 (m-30) cc_final: 0.8692 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0613
  time to fit residues: 11.0732
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  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.085004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.068099 restraints weight = 38329.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.070194 restraints weight = 24215.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.071531 restraints weight = 17180.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.072733 restraints weight = 13606.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.073525 restraints weight = 11088.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.4507

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= 0.121
  Angle     :  0.564   9.564  11204  Z= 0.298
  Chirality :  0.042   0.176   1200
  Planarity :  0.005   0.038   1432
  Dihedral  :  5.318  39.150   1104
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.28), residues: 980
  helix:  1.60 (0.24), residues: 458
  sheet: -1.53 (0.50), residues: 122
  loop : -1.90 (0.32), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 799 
 TYR   0.013   0.001   TYR B 946 
 PHE   0.008   0.001   PHE B 710 
 TRP   0.014   0.002   TRP B1189 
 HIS   0.002   0.001   HIS A 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8286)
  covalent geometry    : angle       0.56420 (11204)
  hydrogen bonds       : bond        0.03763 (  382)
  hydrogen bonds       : angle       4.02645 ( 1077)

*********************** 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
  126 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8901 (p0) cc_final: 0.6773 (p0)
REVERT: A  714 MET cc_start: 0.8319 (mpp) cc_final: 0.7841 (mpp)
REVERT: A  818 ASP cc_start: 0.8393 (m-30) cc_final: 0.8144 (m-30)
REVERT: A  833 GLU cc_start: 0.8517 (pt0) cc_final: 0.8172 (pt0)
REVERT: A  846 MET cc_start: 0.8259 (ttp) cc_final: 0.8043 (ttm)
REVERT: A  856 TRP cc_start: 0.3846 (p-90) cc_final: 0.2722 (p-90)
REVERT: A  882 LYS cc_start: 0.8924 (pttt) cc_final: 0.8515 (ptpp)
REVERT: A  905 ASN cc_start: 0.8797 (m110) cc_final: 0.8462 (m-40)
REVERT: A  917 TYR cc_start: 0.9113 (m-10) cc_final: 0.8825 (m-80)
REVERT: A  957 MET cc_start: 0.9524 (mmm) cc_final: 0.9090 (mmm)
REVERT: A 1038 TYR cc_start: 0.8856 (m-80) cc_final: 0.8564 (m-10)
REVERT: A 1112 GLU cc_start: 0.9333 (mp0) cc_final: 0.9071 (mp0)
REVERT: A 1125 ILE cc_start: 0.9034 (mt) cc_final: 0.8686 (tp)
REVERT: A 1132 GLU cc_start: 0.8324 (tt0) cc_final: 0.7882 (tp30)
REVERT: A 1153 ASP cc_start: 0.9021 (m-30) cc_final: 0.8800 (m-30)
REVERT: B  712 ASP cc_start: 0.8858 (p0) cc_final: 0.6729 (p0)
REVERT: B  714 MET cc_start: 0.8320 (mpp) cc_final: 0.7898 (mpp)
REVERT: B  833 GLU cc_start: 0.8340 (pt0) cc_final: 0.8038 (tt0)
REVERT: B  856 TRP cc_start: 0.4039 (p-90) cc_final: 0.3308 (p-90)
REVERT: B  905 ASN cc_start: 0.8785 (m110) cc_final: 0.8480 (m-40)
REVERT: B  917 TYR cc_start: 0.8979 (m-10) cc_final: 0.8712 (m-80)
REVERT: B  956 ARG cc_start: 0.9120 (mmt90) cc_final: 0.8903 (mmt90)
REVERT: B  957 MET cc_start: 0.9504 (mmm) cc_final: 0.9041 (mmm)
REVERT: B  966 TYR cc_start: 0.5491 (m-80) cc_final: 0.5221 (m-80)
REVERT: B  990 PHE cc_start: 0.8585 (m-10) cc_final: 0.8216 (m-10)
REVERT: B 1038 TYR cc_start: 0.8710 (m-10) cc_final: 0.8461 (m-10)
REVERT: B 1112 GLU cc_start: 0.9321 (mp0) cc_final: 0.9022 (mp0)
REVERT: B 1128 LEU cc_start: 0.8878 (mt) cc_final: 0.8602 (mt)
REVERT: B 1148 MET cc_start: 0.7329 (mtm) cc_final: 0.7051 (mtp)
REVERT: B 1153 ASP cc_start: 0.8982 (m-30) cc_final: 0.8755 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0688
  time to fit residues: 12.9413
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  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 90 optimal weight:    0.4980
   chunk 8 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.084351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.067709 restraints weight = 39103.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.069622 restraints weight = 25370.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.071051 restraints weight = 18414.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.072080 restraints weight = 14424.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.072744 restraints weight = 11951.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.4552

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= 0.141
  Angle     :  0.593   9.463  11204  Z= 0.313
  Chirality :  0.042   0.182   1200
  Planarity :  0.005   0.037   1432
  Dihedral  :  5.349  41.927   1104
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.28), residues: 980
  helix:  1.53 (0.24), residues: 458
  sheet: -1.48 (0.50), residues: 122
  loop : -1.90 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1039 
 TYR   0.026   0.002   TYR A 769 
 PHE   0.008   0.001   PHE B 750 
 TRP   0.016   0.002   TRP B1189 
 HIS   0.003   0.001   HIS A 774 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8286)
  covalent geometry    : angle       0.59335 (11204)
  hydrogen bonds       : bond        0.03824 (  382)
  hydrogen bonds       : angle       4.12092 ( 1077)

*********************** 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
  123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  712 ASP cc_start: 0.8919 (p0) cc_final: 0.6775 (p0)
REVERT: A  714 MET cc_start: 0.8340 (mpp) cc_final: 0.7822 (mpp)
REVERT: A  818 ASP cc_start: 0.8325 (m-30) cc_final: 0.8112 (m-30)
REVERT: A  833 GLU cc_start: 0.8472 (pt0) cc_final: 0.8170 (pt0)
REVERT: A  856 TRP cc_start: 0.3788 (p-90) cc_final: 0.2251 (p-90)
REVERT: A  882 LYS cc_start: 0.8917 (pttt) cc_final: 0.8512 (ptpp)
REVERT: A  905 ASN cc_start: 0.8823 (m110) cc_final: 0.8497 (m-40)
REVERT: A  917 TYR cc_start: 0.9062 (m-10) cc_final: 0.8827 (m-80)
REVERT: A  957 MET cc_start: 0.9516 (mmm) cc_final: 0.9048 (mmm)
REVERT: A 1038 TYR cc_start: 0.8843 (m-80) cc_final: 0.8550 (m-10)
REVERT: A 1125 ILE cc_start: 0.9049 (mt) cc_final: 0.8668 (tp)
REVERT: A 1132 GLU cc_start: 0.8368 (tt0) cc_final: 0.7853 (tp30)
REVERT: A 1153 ASP cc_start: 0.8967 (m-30) cc_final: 0.8747 (m-30)
REVERT: B  712 ASP cc_start: 0.8833 (p0) cc_final: 0.6680 (p0)
REVERT: B  714 MET cc_start: 0.8379 (mpp) cc_final: 0.7931 (mpp)
REVERT: B  833 GLU cc_start: 0.8337 (pt0) cc_final: 0.8055 (tt0)
REVERT: B  856 TRP cc_start: 0.3935 (p-90) cc_final: 0.3264 (p-90)
REVERT: B  905 ASN cc_start: 0.8777 (m110) cc_final: 0.8471 (m-40)
REVERT: B  917 TYR cc_start: 0.8940 (m-10) cc_final: 0.8692 (m-80)
REVERT: B  957 MET cc_start: 0.9509 (mmm) cc_final: 0.9043 (mmm)
REVERT: B  966 TYR cc_start: 0.5529 (m-80) cc_final: 0.5249 (m-80)
REVERT: B 1038 TYR cc_start: 0.8677 (m-10) cc_final: 0.8445 (m-10)
REVERT: B 1060 MET cc_start: 0.7947 (tmm) cc_final: 0.7663 (tmm)
REVERT: B 1112 GLU cc_start: 0.9316 (mp0) cc_final: 0.8989 (mp0)
REVERT: B 1125 ILE cc_start: 0.8474 (mt) cc_final: 0.8155 (tp)
REVERT: B 1128 LEU cc_start: 0.8893 (mt) cc_final: 0.8628 (mt)
REVERT: B 1148 MET cc_start: 0.7332 (mtm) cc_final: 0.7005 (ttm)
REVERT: B 1153 ASP cc_start: 0.8934 (m-30) cc_final: 0.8717 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0737
  time to fit residues: 13.3629
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  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 34 optimal weight:    6.9990
   chunk 93 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 70 optimal weight:    0.3980
   chunk 79 optimal weight:    0.0980
   chunk 9 optimal weight:    0.0670
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 753 HIS
B 774 HIS
B 887 HIS
** B1075 ASN ** 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 = 0.4011 r_free = 0.4011 target = 0.087331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.070137 restraints weight = 37382.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.072174 restraints weight = 24296.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.073686 restraints weight = 17750.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.074861 restraints weight = 13960.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.075697 restraints weight = 11433.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.4931

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= 0.105
  Angle     :  0.553   8.958  11204  Z= 0.286
  Chirality :  0.041   0.158   1200
  Planarity :  0.004   0.041   1432
  Dihedral  :  5.043  41.839   1104
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.28), residues: 980
  helix:  1.76 (0.24), residues: 458
  sheet: -1.55 (0.49), residues: 126
  loop : -1.72 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 799 
 TYR   0.011   0.001   TYR B 966 
 PHE   0.020   0.001   PHE B 710 
 TRP   0.011   0.001   TRP B1189 
 HIS   0.003   0.001   HIS B 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 8286)
  covalent geometry    : angle       0.55250 (11204)
  hydrogen bonds       : bond        0.03606 (  382)
  hydrogen bonds       : angle       3.92253 ( 1077)

********************** 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
  133 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  703 ILE cc_start: 0.7140 (mt) cc_final: 0.6803 (mm)
REVERT: A  712 ASP cc_start: 0.9019 (p0) cc_final: 0.6688 (p0)
REVERT: A  714 MET cc_start: 0.8310 (mpp) cc_final: 0.7730 (mpp)
REVERT: A  741 PHE cc_start: 0.8125 (t80) cc_final: 0.7903 (t80)
REVERT: A  814 PHE cc_start: 0.8123 (m-80) cc_final: 0.7807 (m-80)
REVERT: A  833 GLU cc_start: 0.8362 (pt0) cc_final: 0.8017 (tt0)
REVERT: A  856 TRP cc_start: 0.3692 (p-90) cc_final: 0.2609 (p-90)
REVERT: A  882 LYS cc_start: 0.8839 (pttt) cc_final: 0.8436 (ptpp)
REVERT: A  905 ASN cc_start: 0.8806 (m110) cc_final: 0.8520 (m-40)
REVERT: A  917 TYR cc_start: 0.8975 (m-10) cc_final: 0.8714 (m-80)
REVERT: A  957 MET cc_start: 0.9503 (mmm) cc_final: 0.9057 (mmm)
REVERT: A 1038 TYR cc_start: 0.8800 (m-80) cc_final: 0.8514 (m-10)
REVERT: A 1112 GLU cc_start: 0.9302 (mp0) cc_final: 0.9007 (mp0)
REVERT: A 1125 ILE cc_start: 0.9021 (mt) cc_final: 0.8597 (tp)
REVERT: A 1128 LEU cc_start: 0.8444 (mm) cc_final: 0.8186 (mm)
REVERT: A 1132 GLU cc_start: 0.8307 (tt0) cc_final: 0.7823 (tp30)
REVERT: B  712 ASP cc_start: 0.9033 (p0) cc_final: 0.6736 (p0)
REVERT: B  714 MET cc_start: 0.8230 (mpp) cc_final: 0.7840 (mpp)
REVERT: B  833 GLU cc_start: 0.8225 (pt0) cc_final: 0.7946 (tt0)
REVERT: B  856 TRP cc_start: 0.3794 (p-90) cc_final: 0.3064 (p-90)
REVERT: B  905 ASN cc_start: 0.8817 (m110) cc_final: 0.8573 (m-40)
REVERT: B  917 TYR cc_start: 0.8852 (m-10) cc_final: 0.8455 (m-80)
REVERT: B  957 MET cc_start: 0.9503 (mmm) cc_final: 0.9050 (mmm)
REVERT: B  966 TYR cc_start: 0.5639 (m-80) cc_final: 0.5357 (m-80)
REVERT: B 1038 TYR cc_start: 0.8678 (m-10) cc_final: 0.8441 (m-10)
REVERT: B 1060 MET cc_start: 0.7918 (tmm) cc_final: 0.7666 (tmm)
REVERT: B 1112 GLU cc_start: 0.9308 (mp0) cc_final: 0.9014 (mp0)
REVERT: B 1125 ILE cc_start: 0.8366 (mt) cc_final: 0.8041 (tp)
REVERT: B 1128 LEU cc_start: 0.8911 (mt) cc_final: 0.8606 (mt)
REVERT: B 1148 MET cc_start: 0.7226 (mtm) cc_final: 0.6996 (mtp)
REVERT: B 1153 ASP cc_start: 0.8923 (m-30) cc_final: 0.8708 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0661
  time to fit residues: 13.3628
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  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 96 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 789 HIS
** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1075 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.084598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.067933 restraints weight = 38864.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.069938 restraints weight = 24737.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.071406 restraints weight = 17824.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.072321 restraints weight = 13864.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.073183 restraints weight = 11615.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.4862

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= 0.140
  Angle     :  0.576   9.644  11204  Z= 0.304
  Chirality :  0.042   0.175   1200
  Planarity :  0.004   0.035   1432
  Dihedral  :  5.169  41.190   1104
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.28), residues: 980
  helix:  1.77 (0.24), residues: 460
  sheet: -1.34 (0.51), residues: 122
  loop : -1.77 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1039 
 TYR   0.029   0.002   TYR A 769 
 PHE   0.013   0.001   PHE B 710 
 TRP   0.017   0.002   TRP B1189 
 HIS   0.015   0.001   HIS A1099 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8286)
  covalent geometry    : angle       0.57585 (11204)
  hydrogen bonds       : bond        0.03630 (  382)
  hydrogen bonds       : angle       3.92265 ( 1077)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1576.02 seconds
wall clock time: 27 minutes 58.78 seconds (1678.78 seconds total)