Starting phenix.real_space_refine
on Wed Feb 12 15:24:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b3o_7040/02_2025/6b3o_7040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b3o_7040/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b3o_7040/02_2025/6b3o_7040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b3o_7040/02_2025/6b3o_7040.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b3o_7040/02_2025/6b3o_7040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b3o_7040/02_2025/6b3o_7040.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B
  Time building chain proxies: 5.17, per 1000 atoms: 0.65
  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=4, 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

  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: 2.25
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.68
  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: 2.37

  Time building geometry restraints manager: 2.58 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: 4706
       15.46 -    30.91: 132
       30.91 -    46.37: 21
       46.37 -    61.82: 36
       61.82 -    77.28: 16
  Dihedral angle restraints: 4911
    sinusoidal: 1893
      harmonic: 3018
  Sorted by residual:
  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 A 780 "
           pdb=" SG  CYS A 780 "
           pdb=" SG  CYS A 786 "
           pdb=" CB  CYS A 786 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.74   35.26     1      1.00e+01 1.00e-02 1.76e+01
  dihedral pdb=" CA  SER A 768 "
           pdb=" C   SER A 768 "
           pdb=" N   PRO A 769 "
           pdb=" CA  PRO A 769 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.67   17.33     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 4908 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:
        2.02 -     2.60: 152
        2.60 -     3.17: 7670
        3.17 -     3.75: 12674
        3.75 -     4.32: 17367
        4.32 -     4.90: 27382
  Nonbonded interactions: 65245
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C1082 "
            pdb=" SG  CYS C1093 "
     model   vdw
     2.021 3.760
  nonbonded pdb=" SG  CYS B1082 "
            pdb=" SG  CYS B1093 "
     model   vdw
     2.022 3.760
  nonbonded pdb=" SG  CYS C 780 "
            pdb=" SG  CYS C 786 "
     model   vdw
     2.022 3.760
  nonbonded pdb=" SG  CYS B 780 "
            pdb=" SG  CYS B 786 "
     model   vdw
     2.022 3.760
  nonbonded pdb=" SG  CYS C 775 "
            pdb=" SG  CYS C 797 "
     model   vdw
     2.033 3.760
  ... (remaining 65240 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  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:             2.610
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.030
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.950
-------------------------------------------------------------------------------
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   8124  Z= 1.595
  Angle     :  1.821  12.890  11034  Z= 1.249
  Chirality :  0.105   0.372   1272
  Planarity :  0.008   0.033   1446
  Dihedral  : 10.994  77.281   2943
  Min Nonbonded Distance : 2.021

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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.24), 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
 TRP   0.043   0.013   TRP A1153 
 HIS   0.014   0.005   HIS B1098 
 PHE   0.045   0.007   PHE A1155 
 TYR   0.032   0.007   TYR B1181 
 ARG   0.008   0.001   ARG C1050 

*********************** 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  : 0.819 
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: 0.2290
  time to fit residues: 66.7082
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  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.160141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.154099 restraints weight = 9537.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.139950 restraints weight = 13651.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139919 restraints weight = 12222.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   8124  Z= 0.308
  Angle     :  0.747   7.992  11034  Z= 0.404
  Chirality :  0.045   0.188   1272
  Planarity :  0.005   0.040   1446
  Dihedral  :  5.234  23.412   1089
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  1.86 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.25), residues: 1020
  helix:  3.32 (0.21), residues: 471
  sheet:  0.63 (0.43), residues: 126
  loop : -0.91 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C1153 
 HIS   0.005   0.002   HIS B 759 
 PHE   0.016   0.002   PHE B 778 
 TYR   0.014   0.002   TYR A1181 
 ARG   0.005   0.001   ARG B1033 

*********************** 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
  154 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8884 (p) cc_final: 0.8422 (t)
REVERT: A  767 ARG cc_start: 0.7459 (ptt-90) cc_final: 0.6435 (ptm160)
REVERT: A 1084 LYS cc_start: 0.8358 (mttt) cc_final: 0.8084 (mttt)
REVERT: A 1153 TRP cc_start: 0.7299 (m100) cc_final: 0.6571 (m100)
REVERT: A 1225 ASN cc_start: 0.7567 (m-40) cc_final: 0.6514 (p0)
REVERT: B  992 ASN cc_start: 0.7254 (t0) cc_final: 0.6842 (m110)
REVERT: B 1084 LYS cc_start: 0.8080 (mttt) cc_final: 0.7659 (mttt)
REVERT: B 1153 TRP cc_start: 0.6725 (m100) cc_final: 0.6456 (m100)
REVERT: B 1237 ARG cc_start: 0.7007 (mtp180) cc_final: 0.6609 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.2127
  time to fit residues: 43.9846
Evaluate side-chains
  99 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 750 GLN
A1055 ASN
B1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.157683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.151927 restraints weight = 9896.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.138944 restraints weight = 15778.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.138051 restraints weight = 16835.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8124  Z= 0.278
  Angle     :  0.653   8.120  11034  Z= 0.351
  Chirality :  0.042   0.151   1272
  Planarity :  0.004   0.035   1446
  Dihedral  :  5.132  24.435   1089
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.65 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.25), residues: 1020
  helix:  3.28 (0.21), residues: 471
  sheet:  0.03 (0.35), residues: 159
  loop : -1.14 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1153 
 HIS   0.004   0.002   HIS A1114 
 PHE   0.017   0.002   PHE C1207 
 TYR   0.017   0.002   TYR C1233 
 ARG   0.003   0.001   ARG A1050 

*********************** 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
  137 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8757 (p) cc_final: 0.8280 (t)
REVERT: A  767 ARG cc_start: 0.7466 (ptt-90) cc_final: 0.6745 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7211 (m100) cc_final: 0.6490 (m100)
REVERT: A 1240 ASP cc_start: 0.7498 (t0) cc_final: 0.7114 (t0)
REVERT: B 1084 LYS cc_start: 0.8060 (mttt) cc_final: 0.7619 (mttt)
REVERT: B 1237 ARG cc_start: 0.6870 (mtp180) cc_final: 0.6329 (mmp80)
REVERT: C 1153 TRP cc_start: 0.6838 (m100) cc_final: 0.6593 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.2036
  time to fit residues: 37.9524
Evaluate side-chains
  87 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0270
   chunk 81 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 57 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 788 GLN
B 801 ASN
B1055 ASN
B1148 GLN
** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 801 ASN
C1170 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.155935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.148766 restraints weight = 9952.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137048 restraints weight = 15305.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136475 restraints weight = 13811.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.4793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8124  Z= 0.272
  Angle     :  0.630   8.097  11034  Z= 0.337
  Chirality :  0.041   0.154   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  5.060  25.520   1089
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.65 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.62 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 1020
  helix:  3.29 (0.21), residues: 471
  sheet:  0.02 (0.40), residues: 123
  loop : -1.23 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C1206 
 HIS   0.005   0.001   HIS A1114 
 PHE   0.017   0.002   PHE B1188 
 TYR   0.019   0.002   TYR B1233 
 ARG   0.002   0.001   ARG C1033 

*********************** 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
  134 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.885 
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: A  766 THR cc_start: 0.8623 (p) cc_final: 0.8117 (t)
REVERT: A  767 ARG cc_start: 0.7700 (ptt-90) cc_final: 0.7012 (ptm160)
REVERT: A 1092 PHE cc_start: 0.8626 (t80) cc_final: 0.8324 (t80)
REVERT: A 1153 TRP cc_start: 0.7489 (m100) cc_final: 0.6535 (m100)
REVERT: A 1240 ASP cc_start: 0.7492 (t0) cc_final: 0.6358 (m-30)
REVERT: B 1084 LYS cc_start: 0.7978 (mttt) cc_final: 0.7557 (mttt)
REVERT: B 1237 ARG cc_start: 0.6854 (mtp180) cc_final: 0.6231 (mmp80)
REVERT: C 1153 TRP cc_start: 0.7125 (m100) cc_final: 0.6673 (m100)
REVERT: C 1240 ASP cc_start: 0.7617 (t0) cc_final: 0.7320 (t70)
  outliers start: 2
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1855
  time to fit residues: 33.9875
Evaluate side-chains
  96 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 96 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1055 ASN
B1055 ASN
C 801 ASN
C1055 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.161770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.157886 restraints weight = 9854.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.155803 restraints weight = 13667.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.154463 restraints weight = 17621.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.5112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8124  Z= 0.304
  Angle     :  0.648   8.118  11034  Z= 0.345
  Chirality :  0.042   0.145   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  5.315  25.334   1089
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.84 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.26), residues: 1020
  helix:  3.12 (0.22), residues: 474
  sheet: -0.17 (0.42), residues: 111
  loop : -1.28 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B1206 
 HIS   0.006   0.002   HIS A1114 
 PHE   0.024   0.002   PHE B1092 
 TYR   0.016   0.002   TYR C1181 
 ARG   0.003   0.001   ARG C1033 

*********************** 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
  138 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.950 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7703 (ptt-90) cc_final: 0.6863 (ptm160)
REVERT: A 1029 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8613 (tm-30)
REVERT: A 1153 TRP cc_start: 0.7230 (m100) cc_final: 0.6468 (m100)
REVERT: B  791 VAL cc_start: 0.7935 (t) cc_final: 0.7688 (t)
REVERT: B 1077 GLU cc_start: 0.6986 (tt0) cc_final: 0.6601 (tt0)
REVERT: B 1084 LYS cc_start: 0.8009 (mttt) cc_final: 0.7627 (mttt)
REVERT: B 1234 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7622 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2000
  time to fit residues: 38.0913
Evaluate side-chains
  92 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 76 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.163277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.157861 restraints weight = 9872.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.146760 restraints weight = 13794.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.146405 restraints weight = 13569.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.5495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8124  Z= 0.245
  Angle     :  0.616   9.252  11034  Z= 0.324
  Chirality :  0.040   0.139   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.064  23.840   1089
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.14 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.26), residues: 1020
  helix:  3.16 (0.22), residues: 474
  sheet:  0.12 (0.37), residues: 138
  loop : -1.27 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1206 
 HIS   0.005   0.002   HIS A1114 
 PHE   0.020   0.002   PHE B1092 
 TYR   0.013   0.002   TYR B1233 
 ARG   0.005   0.001   ARG A1237 

*********************** 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
  133 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7623 (ptt-90) cc_final: 0.7061 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7437 (m100) cc_final: 0.6559 (m100)
REVERT: A 1183 LYS cc_start: 0.7870 (tttt) cc_final: 0.7606 (tttm)
REVERT: A 1237 ARG cc_start: 0.6883 (mmp80) cc_final: 0.6509 (mmp80)
REVERT: B  791 VAL cc_start: 0.7887 (t) cc_final: 0.7586 (t)
REVERT: B 1077 GLU cc_start: 0.7113 (tt0) cc_final: 0.6695 (tt0)
REVERT: B 1084 LYS cc_start: 0.7854 (mttt) cc_final: 0.7416 (mttt)
REVERT: B 1183 LYS cc_start: 0.7927 (tptt) cc_final: 0.7704 (tptp)
REVERT: B 1234 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: B 1240 ASP cc_start: 0.7729 (t0) cc_final: 0.6991 (t0)
REVERT: C 1153 TRP cc_start: 0.7135 (m100) cc_final: 0.6473 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2023
  time to fit residues: 36.6793
Evaluate side-chains
  95 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    0.3980
   chunk 19 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 91 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 801 ASN
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.156370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.150628 restraints weight = 9932.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137851 restraints weight = 14620.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.137149 restraints weight = 15473.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.5676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8124  Z= 0.277
  Angle     :  0.631   7.976  11034  Z= 0.335
  Chirality :  0.041   0.136   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.218  23.315   1089
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.75 %
    Favored  : 96.96 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.26), residues: 1020
  helix:  3.06 (0.22), residues: 480
  sheet:  0.04 (0.40), residues: 126
  loop : -1.29 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C1206 
 HIS   0.006   0.002   HIS C1114 
 PHE   0.019   0.002   PHE B1092 
 TYR   0.013   0.002   TYR A1181 
 ARG   0.003   0.001   ARG C1089 

*********************** 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
  123 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1153 TRP cc_start: 0.7385 (m100) cc_final: 0.6563 (m100)
REVERT: A 1237 ARG cc_start: 0.6727 (mmp80) cc_final: 0.6446 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7317 (tt0) cc_final: 0.6899 (tt0)
REVERT: B 1084 LYS cc_start: 0.7889 (mttt) cc_final: 0.7434 (mttt)
REVERT: C 1153 TRP cc_start: 0.7157 (m100) cc_final: 0.6484 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1983
  time to fit residues: 34.0256
Evaluate side-chains
  83 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 100 optimal weight:    0.9990
   chunk 84 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0070
   chunk 59 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
B 750 GLN
B1055 ASN
C 801 ASN
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 = 0.158242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.150677 restraints weight = 10003.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.137479 restraints weight = 14428.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.137684 restraints weight = 10912.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.5860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8124  Z= 0.220
  Angle     :  0.594   9.915  11034  Z= 0.312
  Chirality :  0.040   0.137   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  4.971  22.632   1089
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.65 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1020
  helix:  3.29 (0.23), residues: 474
  sheet: -0.27 (0.42), residues: 123
  loop : -1.23 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1206 
 HIS   0.005   0.001   HIS A1114 
 PHE   0.019   0.002   PHE A1092 
 TYR   0.013   0.002   TYR B1117 
 ARG   0.003   0.001   ARG B1089 

*********************** 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
  119 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1183 LYS cc_start: 0.7590 (tttt) cc_final: 0.7347 (tttm)
REVERT: A 1235 MET cc_start: 0.7059 (ptp) cc_final: 0.5727 (tmm)
REVERT: A 1237 ARG cc_start: 0.6794 (mmp80) cc_final: 0.6381 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7191 (tt0) cc_final: 0.6798 (tt0)
REVERT: B 1084 LYS cc_start: 0.7691 (mttt) cc_final: 0.7320 (mttt)
REVERT: B 1240 ASP cc_start: 0.8155 (t0) cc_final: 0.7416 (t0)
REVERT: C 1153 TRP cc_start: 0.7198 (m100) cc_final: 0.6493 (m100)
REVERT: C 1177 CYS cc_start: 0.7448 (m) cc_final: 0.7106 (m)
REVERT: C 1237 ARG cc_start: 0.6257 (mmp80) cc_final: 0.6044 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2174
  time to fit residues: 35.4993
Evaluate side-chains
  83 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 85 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 801 ASN
** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1055 ASN
C 750 GLN
** C1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1055 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.151298 restraints weight = 10052.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.137655 restraints weight = 14244.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.137190 restraints weight = 15367.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.5930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8124  Z= 0.250
  Angle     :  0.607   7.800  11034  Z= 0.320
  Chirality :  0.041   0.136   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.098  22.366   1089
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.84 %
    Favored  : 96.86 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.26), residues: 1020
  helix:  3.09 (0.23), residues: 486
  sheet: -0.22 (0.46), residues: 111
  loop : -1.20 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1206 
 HIS   0.006   0.002   HIS C1114 
 PHE   0.030   0.002   PHE C1092 
 TYR   0.013   0.002   TYR B1117 
 ARG   0.002   0.000   ARG B1033 

*********************** 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
  115 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7642 (ptt-90) cc_final: 0.6966 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7272 (m100) cc_final: 0.6222 (m100)
REVERT: A 1235 MET cc_start: 0.6792 (ptp) cc_final: 0.5659 (tmm)
REVERT: B 1077 GLU cc_start: 0.7314 (tt0) cc_final: 0.6849 (tt0)
REVERT: B 1084 LYS cc_start: 0.7828 (mttt) cc_final: 0.7499 (mttt)
REVERT: C 1102 LEU cc_start: 0.8017 (mt) cc_final: 0.7806 (mt)
REVERT: C 1153 TRP cc_start: 0.7150 (m100) cc_final: 0.6449 (m100)
REVERT: C 1237 ARG cc_start: 0.6256 (mmp80) cc_final: 0.6037 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2097
  time to fit residues: 32.7846
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  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 29 optimal weight:    0.2980
   chunk 95 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 801 ASN
** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.157972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.150298 restraints weight = 9906.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.137849 restraints weight = 15384.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137333 restraints weight = 14877.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.6067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8124  Z= 0.238
  Angle     :  0.607  10.366  11034  Z= 0.317
  Chirality :  0.040   0.138   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.018  21.796   1089
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.84 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1020
  helix:  3.20 (0.22), residues: 480
  sheet: -0.39 (0.45), residues: 111
  loop : -1.26 (0.28), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1206 
 HIS   0.005   0.001   HIS A1114 
 PHE   0.025   0.002   PHE C1092 
 TYR   0.018   0.002   TYR A1233 
 ARG   0.003   0.000   ARG B1237 

********************** 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
  115 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7608 (ptt-90) cc_final: 0.7011 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7259 (m100) cc_final: 0.6244 (m100)
REVERT: A 1174 MET cc_start: 0.5129 (mmm) cc_final: 0.4544 (mmm)
REVERT: A 1235 MET cc_start: 0.6813 (ptp) cc_final: 0.5763 (tmm)
REVERT: A 1237 ARG cc_start: 0.6561 (mmp80) cc_final: 0.6278 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7320 (tt0) cc_final: 0.6835 (tt0)
REVERT: B 1084 LYS cc_start: 0.7792 (mttt) cc_final: 0.7399 (mmtp)
REVERT: B 1240 ASP cc_start: 0.8035 (t0) cc_final: 0.7299 (t0)
REVERT: C 1153 TRP cc_start: 0.7138 (m100) cc_final: 0.6424 (m100)
REVERT: C 1237 ARG cc_start: 0.6142 (mmp80) cc_final: 0.5930 (mmp80)
REVERT: C 1239 GLN cc_start: 0.6111 (tt0) cc_final: 0.5890 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.2101
  time to fit residues: 32.5903
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  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 84 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 63 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1055 ASN
C 801 ASN
** C1048 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 = 0.3792 r_free = 0.3792 target = 0.156002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.150168 restraints weight = 9999.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135779 restraints weight = 15284.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.136108 restraints weight = 13109.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.6099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8124  Z= 0.275
  Angle     :  0.632  10.131  11034  Z= 0.332
  Chirality :  0.041   0.138   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  5.138  21.920   1089
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.94 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1020
  helix:  2.99 (0.22), residues: 486
  sheet: -0.66 (0.45), residues: 111
  loop : -1.23 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C1206 
 HIS   0.006   0.001   HIS A1114 
 PHE   0.031   0.002   PHE A1092 
 TYR   0.017   0.002   TYR B1233 
 ARG   0.003   0.000   ARG B1089 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2283.64 seconds
wall clock time: 42 minutes 13.08 seconds (2533.08 seconds total)