Starting phenix.real_space_refine
on Fri Aug 22 21:29:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b3o_7040/08_2025/6b3o_7040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b3o_7040/08_2025/6b3o_7040.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b3o_7040/08_2025/6b3o_7040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b3o_7040/08_2025/6b3o_7040.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b3o_7040/08_2025/6b3o_7040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b3o_7040/08_2025/6b3o_7040.map"
  }
  resolution = 4.1
  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=   0.008
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      36      5.16       5
     C    5040      2.51       5
     N    1335      2.21       5
     O    1569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 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: 7980
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2660
          Classifications: {'peptide': 344}
          Link IDs: {'PTRANS': 13, 'TRANS': 330}
          Chain breaks: 1
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.38, per 1000 atoms: 0.17
  Number of scatterers: 7980
  At special positions: 0
  Unit cell: (70.72, 74.8, 202.64, 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      36     16.00
     O    1569      8.00
     N    1335      7.00
     C    5040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 775 " - pdb=" SG  CYS A 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 780 " - pdb=" SG  CYS A 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1132 " - pdb=" SG  CYS A1177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 775 " - pdb=" SG  CYS B 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 775 " - pdb=" SG  CYS C 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 780 " - pdb=" SG  CYS B 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 780 " - pdb=" SG  CYS C 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1132 " - pdb=" SG  CYS B1177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1132 " - pdb=" SG  CYS C1177 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 289.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      48.0% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 774 through 780
    Processing helix  chain 'A' and resid 783 through 791
    Processing helix  chain 'A' and resid 795 through 807
      removed outlier: 4.265A  pdb=" N   ASN A 799 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 1081
    Processing helix  chain 'A' and resid 1198 through 1204
    Processing helix  chain 'A' and resid 1220 through 1224
    Processing helix  chain 'A' and resid 1231 through 1245
    Processing helix  chain 'B' and resid 774 through 780
    Processing helix  chain 'B' and resid 783 through 791
    Processing helix  chain 'B' and resid 795 through 807
      removed outlier: 4.265A  pdb=" N   ASN B 799 " --> pdb=" O   SER B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 973 through 1081
    Processing helix  chain 'B' and resid 1198 through 1204
    Processing helix  chain 'B' and resid 1220 through 1224
    Processing helix  chain 'B' and resid 1231 through 1245
    Processing helix  chain 'C' and resid 774 through 780
    Processing helix  chain 'C' and resid 783 through 791
    Processing helix  chain 'C' and resid 795 through 807
      removed outlier: 4.265A  pdb=" N   ASN C 799 " --> pdb=" O   SER C 795 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 973 through 1081
    Processing helix  chain 'C' and resid 1198 through 1204
    Processing helix  chain 'C' and resid 1220 through 1224
    Processing helix  chain 'C' and resid 1231 through 1245
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1097 through 1106
      removed outlier: 5.491A  pdb=" N   HIS A1098 " --> pdb=" O   TYR A1117 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR A1117 " --> pdb=" O   HIS A1098 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN A 754 " --> pdb=" O   ILE A1120 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   PHE A1122 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR A1124 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   GLN A 750 " --> pdb=" O   THR A1124 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   ASN C1180 " --> pdb=" O   PHE A 755 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ILE A 757 " --> pdb=" O   ASN C1180 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   THR C1182 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   HIS A 759 " --> pdb=" O   THR C1182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1131 through 1132
      removed outlier: 4.238A  pdb=" N   GLY A1138 " --> pdb=" O   MET A1174 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1144 through 1149
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1180 through 1183
      removed outlier: 7.107A  pdb=" N   GLN B 750 " --> pdb=" O   THR B1124 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR B1124 " --> pdb=" O   GLN B 750 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   PHE B1122 " --> pdb=" O   PRO B 752 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN B 754 " --> pdb=" O   ILE B1120 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR B1117 " --> pdb=" O   HIS B1098 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   HIS B1098 " --> pdb=" O   TYR B1117 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1131 through 1132
      removed outlier: 4.237A  pdb=" N   GLY B1138 " --> pdb=" O   MET B1174 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1144 through 1149
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1180 through 1183
      removed outlier: 7.107A  pdb=" N   GLN C 750 " --> pdb=" O   THR C1124 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR C1124 " --> pdb=" O   GLN C 750 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   PHE C1122 " --> pdb=" O   PRO C 752 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN C 754 " --> pdb=" O   ILE C1120 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR C1117 " --> pdb=" O   HIS C1098 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   HIS C1098 " --> pdb=" O   TYR C1117 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1131 through 1132
      removed outlier: 4.238A  pdb=" N   GLY C1138 " --> pdb=" O   MET C1174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 1144 through 1149

    515 hydrogen bonds defined for protein.
    1485 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: 1.01

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1541
        1.31 -     1.43: 2005
        1.43 -     1.56: 4488
        1.56 -     1.68: 42
        1.68 -     1.81: 48
  Bond restraints: 8124
  Sorted by residual:
  bond pdb=" CB  HIS A 759 "
       pdb=" CG  HIS A 759 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.11e+01
  bond pdb=" CB  HIS C 759 "
       pdb=" CG  HIS C 759 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.10e+01
  bond pdb=" CB  HIS B 759 "
       pdb=" CG  HIS B 759 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.09e+01
  bond pdb=" CB  PHE C 796 "
       pdb=" CG  PHE C 796 "
    ideal  model  delta    sigma   weight residual
    1.502  1.356  0.146 2.30e-02 1.89e+03 4.05e+01
  bond pdb=" CB  PHE B 796 "
       pdb=" CG  PHE B 796 "
    ideal  model  delta    sigma   weight residual
    1.502  1.356  0.146 2.30e-02 1.89e+03 4.04e+01
  ... (remaining 8119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 9484
        2.58 -     5.16: 1374
        5.16 -     7.73: 149
        7.73 -    10.31: 24
       10.31 -    12.89: 3
  Bond angle restraints: 11034
  Sorted by residual:
  angle pdb=" N   TYR B1161 "
        pdb=" CA  TYR B1161 "
        pdb=" C   TYR B1161 "
      ideal   model   delta    sigma   weight residual
     108.79  121.68  -12.89 1.53e+00 4.27e-01 7.10e+01
  angle pdb=" N   TYR A1161 "
        pdb=" CA  TYR A1161 "
        pdb=" C   TYR A1161 "
      ideal   model   delta    sigma   weight residual
     108.79  121.66  -12.87 1.53e+00 4.27e-01 7.08e+01
  angle pdb=" N   TYR C1161 "
        pdb=" CA  TYR C1161 "
        pdb=" C   TYR C1161 "
      ideal   model   delta    sigma   weight residual
     108.79  121.62  -12.83 1.53e+00 4.27e-01 7.03e+01
  angle pdb=" N   ILE C1120 "
        pdb=" CA  ILE C1120 "
        pdb=" C   ILE C1120 "
      ideal   model   delta    sigma   weight residual
     113.53  106.94    6.59 9.80e-01 1.04e+00 4.52e+01
  angle pdb=" N   ILE B1120 "
        pdb=" CA  ILE B1120 "
        pdb=" C   ILE B1120 "
      ideal   model   delta    sigma   weight residual
     113.53  106.95    6.58 9.80e-01 1.04e+00 4.50e+01
  ... (remaining 11029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 4710
       15.46 -    30.91: 144
       30.91 -    46.37: 27
       46.37 -    61.82: 36
       61.82 -    77.28: 18
  Dihedral angle restraints: 4935
    sinusoidal: 1917
      harmonic: 3018
  Sorted by residual:
  dihedral pdb=" CB  CYS C 775 "
           pdb=" SG  CYS C 775 "
           pdb=" SG  CYS C 797 "
           pdb=" CB  CYS C 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.77  -65.77     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" CB  CYS A 775 "
           pdb=" SG  CYS A 775 "
           pdb=" SG  CYS A 797 "
           pdb=" CB  CYS A 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.74  -65.74     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" CB  CYS B 775 "
           pdb=" SG  CYS B 775 "
           pdb=" SG  CYS B 797 "
           pdb=" CB  CYS B 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.72  -65.72     1      1.00e+01 1.00e-02 5.65e+01
  ... (remaining 4932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 704
       0.074 -    0.149: 364
       0.149 -    0.223: 156
       0.223 -    0.297: 39
       0.297 -    0.372: 9
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  GLU A1081 "
            pdb=" N   GLU A1081 "
            pdb=" C   GLU A1081 "
            pdb=" CB  GLU A1081 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  LYS B1078 "
            pdb=" N   LYS B1078 "
            pdb=" C   LYS B1078 "
            pdb=" CB  LYS B1078 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  GLU B1081 "
            pdb=" N   GLU B1081 "
            pdb=" C   GLU B1081 "
            pdb=" CB  GLU B1081 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  ... (remaining 1269 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1155 "   -0.045 2.00e-02 2.50e+03   2.72e-02 1.29e+01
        pdb=" CG  PHE A1155 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1155 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1155 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1155 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1155 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1155 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C1155 "    0.045 2.00e-02 2.50e+03   2.70e-02 1.28e+01
        pdb=" CG  PHE C1155 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE C1155 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE C1155 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE C1155 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE C1155 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C1155 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B1155 "    0.045 2.00e-02 2.50e+03   2.70e-02 1.27e+01
        pdb=" CG  PHE B1155 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE B1155 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B1155 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B1155 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE B1155 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B1155 "    0.026 2.00e-02 2.50e+03
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2608
        2.81 -     3.33: 8103
        3.33 -     3.85: 13493
        3.85 -     4.38: 15988
        4.38 -     4.90: 25029
  Nonbonded interactions: 65221
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1066 "
            pdb=" OG  SER C1063 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER A1063 "
            pdb=" OG1 THR B1066 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER B1063 "
            pdb=" OG1 THR C1066 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" N   LYS B1154 "
            pdb=" O   LYS B1154 "
     model   vdw
     2.396 2.496
  nonbonded pdb=" N   LYS C1154 "
            pdb=" O   LYS C1154 "
     model   vdw
     2.396 2.496
  ... (remaining 65216 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'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.080
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.100
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.024   0.146   8136  Z= 1.356
  Angle     :  1.832  12.890  11058  Z= 1.252
  Chirality :  0.105   0.372   1272
  Planarity :  0.008   0.033   1446
  Dihedral  : 10.994  77.281   2943
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.06 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.34 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.14 (0.24), residues: 1020
  helix:  1.69 (0.21), residues: 474
  sheet:  1.16 (0.42), residues: 129
  loop : -0.44 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C1050 
 TYR   0.032   0.007   TYR B1181 
 PHE   0.045   0.007   PHE A1155 
 TRP   0.043   0.013   TRP A1153 
 HIS   0.014   0.005   HIS B1098 

Details of bonding type rmsd
  covalent geometry    : bond        0.02430 ( 8124)
  covalent geometry    : angle       1.82053 (11034)
  SS BOND              : bond        0.00681 (   12)
  SS BOND              : angle       4.70133 (   24)
  hydrogen bonds       : bond        0.16260 (  515)
  hydrogen bonds       : angle       7.74577 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 220
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.9093 (p) cc_final: 0.8833 (t)
REVERT: A  792 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: A 1153 TRP cc_start: 0.7685 (m100) cc_final: 0.6965 (m100)
REVERT: A 1198 ASP cc_start: 0.7796 (t70) cc_final: 0.7427 (m-30)
REVERT: B  787 ARG cc_start: 0.5704 (tpp-160) cc_final: 0.5480 (tpt170)
REVERT: B 1089 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7619 (mmm-85)
REVERT: B 1153 TRP cc_start: 0.7550 (m100) cc_final: 0.7103 (m100)
REVERT: B 1223 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7281 (mmmt)
REVERT: B 1235 MET cc_start: 0.7751 (mtp) cc_final: 0.7247 (tpp)
REVERT: B 1237 ARG cc_start: 0.6565 (mtp180) cc_final: 0.6324 (mmp80)
REVERT: C 1188 PHE cc_start: 0.7023 (t80) cc_final: 0.6290 (t80)
REVERT: C 1220 ASP cc_start: 0.6912 (t0) cc_final: 0.6697 (t0)
REVERT: C 1235 MET cc_start: 0.7888 (mtp) cc_final: 0.6985 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0890
  time to fit residues: 26.1823
Evaluate side-chains
  88 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0670
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.5118

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.162934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.156893 restraints weight = 9523.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143623 restraints weight = 13502.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.143527 restraints weight = 14369.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.143957 restraints weight = 11618.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.144166 restraints weight = 10199.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8136  Z= 0.186
  Angle     :  0.720   7.910  11058  Z= 0.387
  Chirality :  0.044   0.196   1272
  Planarity :  0.005   0.040   1446
  Dihedral  :  5.154  22.548   1089
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.06 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  2.03 (0.25), residues: 1020
  helix:  3.37 (0.21), residues: 471
  sheet:  0.50 (0.42), residues: 132
  loop : -0.85 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 787 
 TYR   0.013   0.002   TYR C1117 
 PHE   0.015   0.002   PHE C 796 
 TRP   0.014   0.002   TRP C1153 
 HIS   0.003   0.002   HIS B 760 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 8124)
  covalent geometry    : angle       0.71694 (11034)
  SS BOND              : bond        0.00577 (   12)
  SS BOND              : angle       1.60997 (   24)
  hydrogen bonds       : bond        0.06796 (  515)
  hydrogen bonds       : angle       5.14138 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8865 (p) cc_final: 0.8418 (t)
REVERT: A  767 ARG cc_start: 0.7328 (ptt-90) cc_final: 0.6285 (ptm160)
REVERT: A 1069 LYS cc_start: 0.8346 (mttp) cc_final: 0.8137 (mttm)
REVERT: A 1084 LYS cc_start: 0.8283 (mttt) cc_final: 0.7982 (mttt)
REVERT: A 1153 TRP cc_start: 0.7187 (m100) cc_final: 0.6550 (m100)
REVERT: A 1225 ASN cc_start: 0.7420 (m-40) cc_final: 0.6368 (p0)
REVERT: B  992 ASN cc_start: 0.7160 (t0) cc_final: 0.6940 (m-40)
REVERT: B 1084 LYS cc_start: 0.8000 (mttt) cc_final: 0.7601 (mttt)
REVERT: B 1153 TRP cc_start: 0.6821 (m100) cc_final: 0.6353 (m100)
REVERT: B 1188 PHE cc_start: 0.6893 (t80) cc_final: 0.6478 (t80)
REVERT: B 1237 ARG cc_start: 0.7167 (mtp180) cc_final: 0.6853 (mmp80)
REVERT: C 1092 PHE cc_start: 0.8662 (t80) cc_final: 0.8442 (t80)
REVERT: C 1237 ARG cc_start: 0.7156 (mmp80) cc_final: 0.6933 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.0806
  time to fit residues: 16.7648
Evaluate side-chains
  105 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 750 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.150381 restraints weight = 9858.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136416 restraints weight = 13516.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136164 restraints weight = 13437.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.136359 restraints weight = 11661.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136148 restraints weight = 13056.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8136  Z= 0.218
  Angle     :  0.723   8.226  11058  Z= 0.386
  Chirality :  0.044   0.140   1272
  Planarity :  0.004   0.035   1446
  Dihedral  :  5.332  26.150   1089
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.75 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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 (0.25), residues: 1020
  helix:  3.01 (0.21), residues: 471
  sheet:  0.21 (0.36), residues: 150
  loop : -1.46 (0.29), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1033 
 TYR   0.018   0.003   TYR C1181 
 PHE   0.021   0.003   PHE B1207 
 TRP   0.007   0.001   TRP C1153 
 HIS   0.007   0.002   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 ( 8124)
  covalent geometry    : angle       0.71467 (11034)
  SS BOND              : bond        0.00727 (   12)
  SS BOND              : angle       2.41777 (   24)
  hydrogen bonds       : bond        0.06470 (  515)
  hydrogen bonds       : angle       4.86105 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8731 (p) cc_final: 0.8202 (t)
REVERT: A  767 ARG cc_start: 0.7502 (ptt-90) cc_final: 0.6811 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7165 (m100) cc_final: 0.6659 (m100)
REVERT: A 1167 THR cc_start: 0.8202 (p) cc_final: 0.7998 (p)
REVERT: A 1240 ASP cc_start: 0.7641 (t0) cc_final: 0.6423 (m-30)
REVERT: B 1084 LYS cc_start: 0.8199 (mttt) cc_final: 0.7818 (mttt)
REVERT: B 1153 TRP cc_start: 0.7095 (m100) cc_final: 0.6738 (m100)
REVERT: B 1237 ARG cc_start: 0.6779 (mtp180) cc_final: 0.6199 (mmp80)
REVERT: C 1153 TRP cc_start: 0.6977 (m100) cc_final: 0.6537 (m100)
REVERT: C 1170 ASN cc_start: 0.7220 (m110) cc_final: 0.6975 (m110)
REVERT: C 1237 ARG cc_start: 0.6824 (mmp80) cc_final: 0.6335 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.0767
  time to fit residues: 14.6977
Evaluate side-chains
  90 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 71 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 79 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A1170 ASN
B1055 ASN
C 788 GLN
C1055 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.152430 restraints weight = 10112.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.140465 restraints weight = 14431.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.140230 restraints weight = 15585.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.140230 restraints weight = 12946.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.140230 restraints weight = 12897.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.4717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8136  Z= 0.175
  Angle     :  0.623   8.006  11058  Z= 0.336
  Chirality :  0.041   0.158   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  5.045  25.507   1089
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.94 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.46 (0.25), residues: 1020
  helix:  3.17 (0.21), residues: 471
  sheet: -0.00 (0.40), residues: 123
  loop : -1.40 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 787 
 TYR   0.018   0.002   TYR B1233 
 PHE   0.016   0.002   PHE C1207 
 TRP   0.006   0.001   TRP C1153 
 HIS   0.004   0.001   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8124)
  covalent geometry    : angle       0.61938 (11034)
  SS BOND              : bond        0.00596 (   12)
  SS BOND              : angle       1.54881 (   24)
  hydrogen bonds       : bond        0.06053 (  515)
  hydrogen bonds       : angle       4.63454 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8603 (p) cc_final: 0.8112 (t)
REVERT: A  767 ARG cc_start: 0.7670 (ptt-90) cc_final: 0.7016 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7379 (m100) cc_final: 0.6490 (m100)
REVERT: B  791 VAL cc_start: 0.7673 (t) cc_final: 0.7441 (t)
REVERT: B 1084 LYS cc_start: 0.7938 (mttt) cc_final: 0.7516 (mttt)
REVERT: B 1167 THR cc_start: 0.8328 (p) cc_final: 0.7912 (p)
REVERT: B 1234 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: B 1237 ARG cc_start: 0.6910 (mtp180) cc_final: 0.6285 (mmp80)
REVERT: C 1092 PHE cc_start: 0.8639 (t80) cc_final: 0.8151 (t80)
REVERT: C 1153 TRP cc_start: 0.7145 (m100) cc_final: 0.6631 (m100)
REVERT: C 1240 ASP cc_start: 0.6729 (t70) cc_final: 0.6433 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0838
  time to fit residues: 14.4740
Evaluate side-chains
  85 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 78 optimal weight:    0.3980
   chunk 87 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN
C1170 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.165266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.163838 restraints weight = 9992.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.163030 restraints weight = 14128.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.162426 restraints weight = 20791.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.147693 restraints weight = 21746.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.147704 restraints weight = 19169.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.5144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8136  Z= 0.167
  Angle     :  0.618   8.016  11058  Z= 0.329
  Chirality :  0.041   0.143   1272
  Planarity :  0.004   0.035   1446
  Dihedral  :  5.023  25.324   1089
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.43 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  2.82 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.44 (0.26), residues: 1020
  helix:  3.07 (0.22), residues: 474
  sheet:  0.05 (0.36), residues: 138
  loop : -1.40 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A1237 
 TYR   0.012   0.002   TYR A1181 
 PHE   0.016   0.002   PHE A1155 
 TRP   0.005   0.001   TRP C1206 
 HIS   0.006   0.002   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8124)
  covalent geometry    : angle       0.61188 (11034)
  SS BOND              : bond        0.00398 (   12)
  SS BOND              : angle       1.95027 (   24)
  hydrogen bonds       : bond        0.05894 (  515)
  hydrogen bonds       : angle       4.47644 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7624 (ptt-90) cc_final: 0.6954 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7241 (m100) cc_final: 0.6606 (m100)
REVERT: A 1231 LEU cc_start: 0.6683 (mt) cc_final: 0.6427 (mm)
REVERT: A 1237 ARG cc_start: 0.7236 (mmp80) cc_final: 0.6781 (mmp80)
REVERT: B  791 VAL cc_start: 0.7880 (t) cc_final: 0.7643 (t)
REVERT: B 1077 GLU cc_start: 0.6990 (tt0) cc_final: 0.6574 (tt0)
REVERT: B 1084 LYS cc_start: 0.7872 (mttt) cc_final: 0.7516 (mttt)
REVERT: B 1237 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6409 (mmp80)
REVERT: B 1240 ASP cc_start: 0.7658 (t0) cc_final: 0.7152 (t0)
REVERT: C 1132 CYS cc_start: 0.4255 (t) cc_final: 0.3992 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 128
  average time/residue: 0.0862
  time to fit residues: 15.0074
Evaluate side-chains
  88 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 43 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0270
   chunk 44 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.165910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.163780 restraints weight = 9789.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.150503 restraints weight = 13914.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.149291 restraints weight = 16125.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.149296 restraints weight = 16602.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.149483 restraints weight = 13742.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.5352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8136  Z= 0.153
  Angle     :  0.594  10.136  11058  Z= 0.314
  Chirality :  0.040   0.149   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  4.866  23.822   1089
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.14 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.50 (0.26), residues: 1020
  helix:  3.09 (0.22), residues: 480
  sheet:  0.09 (0.37), residues: 138
  loop : -1.41 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C1237 
 TYR   0.020   0.002   TYR B1233 
 PHE   0.014   0.002   PHE A1092 
 TRP   0.006   0.001   TRP C1206 
 HIS   0.005   0.001   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8124)
  covalent geometry    : angle       0.58896 (11034)
  SS BOND              : bond        0.00345 (   12)
  SS BOND              : angle       1.82940 (   24)
  hydrogen bonds       : bond        0.05792 (  515)
  hydrogen bonds       : angle       4.36835 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7655 (ptt-90) cc_final: 0.6862 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7372 (m100) cc_final: 0.6551 (m100)
REVERT: A 1183 LYS cc_start: 0.7712 (tttt) cc_final: 0.7417 (tttm)
REVERT: A 1237 ARG cc_start: 0.7060 (mmp80) cc_final: 0.6698 (mmp80)
REVERT: B  791 VAL cc_start: 0.7811 (t) cc_final: 0.7530 (t)
REVERT: B 1077 GLU cc_start: 0.7314 (tt0) cc_final: 0.6815 (tt0)
REVERT: B 1084 LYS cc_start: 0.7824 (mttt) cc_final: 0.7486 (mttt)
REVERT: C 1092 PHE cc_start: 0.8545 (t80) cc_final: 0.8107 (t80)
REVERT: C 1132 CYS cc_start: 0.4293 (t) cc_final: 0.3976 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0899
  time to fit residues: 15.6387
Evaluate side-chains
  85 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    0.1980
   chunk 47 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN
C1170 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.164451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162334 restraints weight = 9915.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161226 restraints weight = 13753.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.160811 restraints weight = 19696.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.160739 restraints weight = 16018.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.149256 restraints weight = 13399.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.5531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8136  Z= 0.163
  Angle     :  0.604   7.804  11058  Z= 0.320
  Chirality :  0.041   0.176   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  4.887  23.130   1089
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.14 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.45 (0.26), residues: 1020
  helix:  3.08 (0.22), residues: 477
  sheet:  0.04 (0.38), residues: 138
  loop : -1.44 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C1237 
 TYR   0.012   0.002   TYR C1117 
 PHE   0.017   0.002   PHE C1155 
 TRP   0.008   0.001   TRP C1206 
 HIS   0.006   0.001   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 8124)
  covalent geometry    : angle       0.59934 (11034)
  SS BOND              : bond        0.00439 (   12)
  SS BOND              : angle       1.72416 (   24)
  hydrogen bonds       : bond        0.05808 (  515)
  hydrogen bonds       : angle       4.38034 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7603 (ptt-90) cc_final: 0.6848 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7327 (m100) cc_final: 0.6492 (m100)
REVERT: B 1077 GLU cc_start: 0.7387 (tt0) cc_final: 0.6850 (tt0)
REVERT: B 1084 LYS cc_start: 0.7907 (mttt) cc_final: 0.7600 (mttt)
REVERT: B 1240 ASP cc_start: 0.7790 (t0) cc_final: 0.7220 (t0)
REVERT: C 1092 PHE cc_start: 0.8429 (t80) cc_final: 0.7986 (t80)
REVERT: C 1132 CYS cc_start: 0.4260 (t) cc_final: 0.4038 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0819
  time to fit residues: 13.2724
Evaluate side-chains
  84 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.155515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149859 restraints weight = 10075.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.136632 restraints weight = 15082.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.136526 restraints weight = 13698.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.136727 restraints weight = 12094.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.136940 restraints weight = 10314.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.5695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8136  Z= 0.203
  Angle     :  0.682   9.671  11058  Z= 0.359
  Chirality :  0.043   0.146   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.264  24.655   1089
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.16 (0.26), residues: 1020
  helix:  2.85 (0.23), residues: 480
  sheet: -0.23 (0.40), residues: 126
  loop : -1.53 (0.27), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B1237 
 TYR   0.018   0.002   TYR B1233 
 PHE   0.020   0.003   PHE A1092 
 TRP   0.007   0.001   TRP C1206 
 HIS   0.006   0.002   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8124)
  covalent geometry    : angle       0.67468 (11034)
  SS BOND              : bond        0.00498 (   12)
  SS BOND              : angle       2.21141 (   24)
  hydrogen bonds       : bond        0.06042 (  515)
  hydrogen bonds       : angle       4.55108 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1153 TRP cc_start: 0.7407 (m100) cc_final: 0.6602 (m100)
REVERT: A 1237 ARG cc_start: 0.6771 (mmp80) cc_final: 0.6329 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7396 (tt0) cc_final: 0.7073 (tt0)
REVERT: B 1084 LYS cc_start: 0.7991 (mttt) cc_final: 0.7646 (mttt)
REVERT: C 1092 PHE cc_start: 0.8476 (t80) cc_final: 0.8024 (t80)
REVERT: C 1132 CYS cc_start: 0.4211 (t) cc_final: 0.3991 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0822
  time to fit residues: 13.4124
Evaluate side-chains
  84 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 801 ASN
B1055 ASN
** B1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.147910 restraints weight = 10117.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 78)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.134159 restraints weight = 14888.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134245 restraints weight = 12450.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134175 restraints weight = 12371.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134179 restraints weight = 10937.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.5799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   8136  Z= 0.225
  Angle     :  0.714  10.168  11058  Z= 0.376
  Chirality :  0.044   0.143   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.496  25.326   1089
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  4.02 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  0.91 (0.26), residues: 1020
  helix:  2.75 (0.23), residues: 471
  sheet: -0.49 (0.41), residues: 126
  loop : -1.66 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1237 
 TYR   0.017   0.002   TYR B1233 
 PHE   0.029   0.003   PHE A1092 
 TRP   0.008   0.001   TRP C1206 
 HIS   0.008   0.002   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 8124)
  covalent geometry    : angle       0.70228 (11034)
  SS BOND              : bond        0.00524 (   12)
  SS BOND              : angle       2.81349 (   24)
  hydrogen bonds       : bond        0.06168 (  515)
  hydrogen bonds       : angle       4.66075 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1174 MET cc_start: 0.5326 (mmm) cc_final: 0.4925 (mmm)
REVERT: A 1237 ARG cc_start: 0.6851 (mmp80) cc_final: 0.6296 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7494 (tt0) cc_final: 0.7214 (tt0)
REVERT: B 1084 LYS cc_start: 0.7924 (mttt) cc_final: 0.7577 (mttt)
REVERT: B 1240 ASP cc_start: 0.8141 (t0) cc_final: 0.7599 (t0)
REVERT: C 1092 PHE cc_start: 0.8470 (t80) cc_final: 0.8018 (t80)
REVERT: C 1237 ARG cc_start: 0.6068 (mmp80) cc_final: 0.5764 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0743
  time to fit residues: 11.2019
Evaluate side-chains
  80 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0770
   chunk 37 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 99 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0070
   chunk 68 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.4356

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.159152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.153622 restraints weight = 9887.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.140834 restraints weight = 14687.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.140374 restraints weight = 15591.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.140614 restraints weight = 12710.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.140702 restraints weight = 11224.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8136  Z= 0.144
  Angle     :  0.594   9.608  11058  Z= 0.312
  Chirality :  0.040   0.140   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  4.961  22.264   1089
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.63 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.29 (0.26), residues: 1020
  helix:  3.24 (0.23), residues: 468
  sheet: -0.40 (0.40), residues: 126
  loop : -1.64 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B1050 
 TYR   0.018   0.002   TYR B1233 
 PHE   0.024   0.002   PHE A1092 
 TRP   0.008   0.001   TRP C1206 
 HIS   0.003   0.001   HIS C1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 8124)
  covalent geometry    : angle       0.58832 (11034)
  SS BOND              : bond        0.00362 (   12)
  SS BOND              : angle       1.92635 (   24)
  hydrogen bonds       : bond        0.05686 (  515)
  hydrogen bonds       : angle       4.37703 ( 1485)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1153 TRP cc_start: 0.7229 (m100) cc_final: 0.6301 (m100)
REVERT: A 1174 MET cc_start: 0.4641 (mmm) cc_final: 0.4289 (mmm)
REVERT: A 1237 ARG cc_start: 0.6655 (mmp80) cc_final: 0.6246 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7286 (tt0) cc_final: 0.6888 (tt0)
REVERT: B 1084 LYS cc_start: 0.7725 (mttt) cc_final: 0.7382 (mttt)
REVERT: C 1092 PHE cc_start: 0.8332 (t80) cc_final: 0.7815 (t80)
REVERT: C 1132 CYS cc_start: 0.4252 (t) cc_final: 0.4013 (t)
REVERT: C 1237 ARG cc_start: 0.5994 (mmp80) cc_final: 0.5779 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0800
  time to fit residues: 12.9449
Evaluate side-chains
  86 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 60 optimal weight:    0.2980
   chunk 56 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 73 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0970
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
B1170 ASN
C 750 GLN
C1055 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.159286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153582 restraints weight = 9762.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.140293 restraints weight = 14120.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140287 restraints weight = 12460.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.140471 restraints weight = 11493.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.140707 restraints weight = 10144.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.6048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8136  Z= 0.144
  Angle     :  0.590   9.238  11058  Z= 0.309
  Chirality :  0.040   0.139   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  4.868  21.649   1089
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.82 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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:  1.26 (0.26), residues: 1020
  helix:  3.04 (0.23), residues: 480
  sheet: -0.41 (0.40), residues: 126
  loop : -1.56 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C1237 
 TYR   0.012   0.001   TYR B1117 
 PHE   0.024   0.002   PHE C 977 
 TRP   0.007   0.001   TRP C1206 
 HIS   0.004   0.001   HIS A1114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8124)
  covalent geometry    : angle       0.58371 (11034)
  SS BOND              : bond        0.00353 (   12)
  SS BOND              : angle       1.90569 (   24)
  hydrogen bonds       : bond        0.05670 (  515)
  hydrogen bonds       : angle       4.34292 ( 1485)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1108.80 seconds
wall clock time: 19 minutes 53.74 seconds (1193.74 seconds total)