Starting phenix.real_space_refine
on Wed Mar 12 15:55:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b3o_7040/03_2025/6b3o_7040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b3o_7040/03_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_7040/03_2025/6b3o_7040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b3o_7040/03_2025/6b3o_7040.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b3o_7040/03_2025/6b3o_7040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b3o_7040/03_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-5624/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: 5.39, per 1000 atoms: 0.68
  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 C 775 " - pdb=" SG  CYS C 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 775 " - pdb=" SG  CYS B 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 780 " - pdb=" SG  CYS C 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 780 " - pdb=" SG  CYS B 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1132 " - pdb=" SG  CYS C1177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1132 " - pdb=" SG  CYS B1177 " 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: 2.16
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.84
  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: 2.42

  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: 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: 0.06
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:             2.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.610
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.400
-------------------------------------------------------------------------------
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= 1.600
  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 : 2.285

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 (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  : 0.865 
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: 0.2249
  time to fit residues: 65.4452
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  : 0.856 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   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:    0.8980
   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 = 0.3828 r_free = 0.3828 target = 0.161061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.155033 restraints weight = 9487.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140467 restraints weight = 13648.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140582 restraints weight = 12170.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
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   0.049   8124  Z= 0.299
  Angle     :  0.740   8.029  11034  Z= 0.400
  Chirality :  0.044   0.189   1272
  Planarity :  0.005   0.038   1446
  Dihedral  :  5.224  23.261   1089
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.16 %
    Favored  : 97.55 %
  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 (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:  1.93 (0.25), residues: 1020
  helix:  3.30 (0.21), residues: 471
  sheet:  0.38 (0.42), residues: 132
  loop : -0.88 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C1153 
 HIS   0.004   0.002   HIS B 760 
 PHE   0.016   0.002   PHE C 796 
 TYR   0.015   0.002   TYR C1117 
 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
  152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8886 (p) cc_final: 0.8432 (t)
REVERT: A  767 ARG cc_start: 0.7405 (ptt-90) cc_final: 0.6356 (ptm160)
REVERT: A 1069 LYS cc_start: 0.8379 (mttp) cc_final: 0.8164 (mttm)
REVERT: A 1084 LYS cc_start: 0.8355 (mttt) cc_final: 0.8062 (mttt)
REVERT: A 1153 TRP cc_start: 0.7289 (m100) cc_final: 0.6468 (m100)
REVERT: A 1198 ASP cc_start: 0.6543 (t70) cc_final: 0.6334 (m-30)
REVERT: A 1225 ASN cc_start: 0.7519 (m-40) cc_final: 0.6415 (p0)
REVERT: B  992 ASN cc_start: 0.7281 (t0) cc_final: 0.6760 (m110)
REVERT: B 1084 LYS cc_start: 0.8076 (mttt) cc_final: 0.7686 (mttt)
REVERT: B 1153 TRP cc_start: 0.6731 (m100) cc_final: 0.6273 (m100)
REVERT: B 1237 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6552 (mmp80)
REVERT: C 1092 PHE cc_start: 0.8684 (t80) cc_final: 0.8434 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2152
  time to fit residues: 43.8102
Evaluate side-chains
  102 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.5978

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.159367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153675 restraints weight = 9838.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140296 restraints weight = 14857.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140322 restraints weight = 12419.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8124  Z= 0.267
  Angle     :  0.652   8.072  11034  Z= 0.349
  Chirality :  0.042   0.157   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.035  24.210   1089
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.65 %
    Favored  : 97.06 %
  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:  1.61 (0.25), residues: 1020
  helix:  3.18 (0.21), residues: 471
  sheet:  0.09 (0.35), residues: 159
  loop : -1.27 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1153 
 HIS   0.004   0.001   HIS C1114 
 PHE   0.016   0.002   PHE C1207 
 TYR   0.017   0.002   TYR C1233 
 ARG   0.003   0.001   ARG B 787 

*********************** 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
  135 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8738 (p) cc_final: 0.8276 (t)
REVERT: A  767 ARG cc_start: 0.7350 (ptt-90) cc_final: 0.6691 (ptm160)
REVERT: A 1084 LYS cc_start: 0.8359 (mttt) cc_final: 0.8155 (mttt)
REVERT: A 1153 TRP cc_start: 0.7229 (m100) cc_final: 0.6488 (m100)
REVERT: A 1233 TYR cc_start: 0.6972 (t80) cc_final: 0.6757 (t80)
REVERT: A 1240 ASP cc_start: 0.7552 (t0) cc_final: 0.7141 (t0)
REVERT: B 1084 LYS cc_start: 0.8039 (mttt) cc_final: 0.7563 (mttt)
REVERT: B 1153 TRP cc_start: 0.7081 (m100) cc_final: 0.6737 (m100)
REVERT: B 1237 ARG cc_start: 0.6841 (mtp180) cc_final: 0.6303 (mmp80)
REVERT: C 1153 TRP cc_start: 0.6985 (m100) cc_final: 0.6544 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2559
  time to fit residues: 47.1230
Evaluate side-chains
  89 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 101 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 750 GLN
A1055 ASN
** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 788 GLN
** C1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145110 restraints weight = 10247.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.142534 restraints weight = 15947.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141307 restraints weight = 19010.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   8124  Z= 0.427
  Angle     :  0.797   8.227  11034  Z= 0.425
  Chirality :  0.046   0.155   1272
  Planarity :  0.005   0.038   1446
  Dihedral  :  5.779  27.891   1089
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.24 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  3.84 %
    Favored  : 95.82 %
  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:  0.88 (0.25), residues: 1020
  helix:  2.56 (0.21), residues: 480
  sheet: -0.40 (0.36), residues: 138
  loop : -1.62 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C1153 
 HIS   0.008   0.002   HIS A1114 
 PHE   0.030   0.003   PHE B1188 
 TYR   0.025   0.003   TYR C1181 
 ARG   0.004   0.001   ARG C1089 

*********************** 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
  123 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7806 (ptt-90) cc_final: 0.7069 (ptm160)
REVERT: A  788 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7374 (mm-40)
REVERT: A 1153 TRP cc_start: 0.7288 (m100) cc_final: 0.6607 (m100)
REVERT: B  791 VAL cc_start: 0.7623 (t) cc_final: 0.7385 (t)
REVERT: B 1084 LYS cc_start: 0.8184 (mttt) cc_final: 0.7776 (mttt)
REVERT: B 1153 TRP cc_start: 0.7057 (m100) cc_final: 0.6827 (m100)
REVERT: C 1029 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: C 1153 TRP cc_start: 0.6873 (m100) cc_final: 0.6167 (m100)
REVERT: C 1240 ASP cc_start: 0.6474 (t0) cc_final: 0.6230 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 123
  average time/residue: 0.2001
  time to fit residues: 33.6399
Evaluate side-chains
  83 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0770
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0970
   overall best weight:    0.4336

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.165467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.146733 restraints weight = 99331.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.148463 restraints weight = 68591.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.148323 restraints weight = 56026.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.5222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8124  Z= 0.214
  Angle     :  0.591   7.906  11034  Z= 0.317
  Chirality :  0.040   0.138   1272
  Planarity :  0.004   0.035   1446
  Dihedral  :  5.134  25.435   1089
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.84 %
    Favored  : 96.86 %
  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 (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:  1.27 (0.26), residues: 1020
  helix:  3.02 (0.22), residues: 474
  sheet: -0.27 (0.36), residues: 153
  loop : -1.55 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C1206 
 HIS   0.005   0.002   HIS B 759 
 PHE   0.016   0.002   PHE A1188 
 TYR   0.012   0.002   TYR C1162 
 ARG   0.003   0.001   ARG B1050 

*********************** 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
  122 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  788 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7381 (mm-40)
REVERT: A 1029 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8528 (tm-30)
REVERT: A 1153 TRP cc_start: 0.7456 (m100) cc_final: 0.6624 (m100)
REVERT: A 1183 LYS cc_start: 0.7910 (tttt) cc_final: 0.7700 (tttm)
REVERT: A 1237 ARG cc_start: 0.7111 (mmp80) cc_final: 0.6727 (mmp80)
REVERT: B  791 VAL cc_start: 0.8028 (t) cc_final: 0.7787 (t)
REVERT: B 1077 GLU cc_start: 0.6992 (tt0) cc_final: 0.6700 (tt0)
REVERT: B 1084 LYS cc_start: 0.7935 (mttt) cc_final: 0.7628 (mttt)
REVERT: B 1240 ASP cc_start: 0.7384 (t0) cc_final: 0.6959 (t0)
REVERT: C 1234 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7371 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.2070
  time to fit residues: 34.1760
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  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 101 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 76 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 6 optimal weight:    0.2980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1055 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.151484 restraints weight = 9924.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.139034 restraints weight = 14929.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.138982 restraints weight = 15622.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.5452

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= 0.278
  Angle     :  0.633   8.014  11034  Z= 0.336
  Chirality :  0.041   0.139   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.135  24.524   1089
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.14 %
    Favored  : 96.57 %
  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:  1.26 (0.26), residues: 1020
  helix:  2.91 (0.22), residues: 474
  sheet:  0.03 (0.38), residues: 138
  loop : -1.52 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C1206 
 HIS   0.005   0.002   HIS C1114 
 PHE   0.015   0.002   PHE B1188 
 TYR   0.014   0.002   TYR A1181 
 ARG   0.003   0.001   ARG B1237 

*********************** 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
  121 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7625 (ptt-90) cc_final: 0.6892 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7294 (m100) cc_final: 0.6502 (m100)
REVERT: A 1183 LYS cc_start: 0.7766 (tttt) cc_final: 0.7471 (tttm)
REVERT: A 1237 ARG cc_start: 0.7161 (mmp80) cc_final: 0.6658 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7432 (tt0) cc_final: 0.6871 (tt0)
REVERT: B 1084 LYS cc_start: 0.8004 (mttt) cc_final: 0.7704 (mttt)
REVERT: C 1092 PHE cc_start: 0.8523 (t80) cc_final: 0.8122 (t80)
REVERT: C 1153 TRP cc_start: 0.7027 (m100) cc_final: 0.6263 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2158
  time to fit residues: 35.4417
Evaluate side-chains
  91 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 60 optimal weight:    0.7980
   chunk 22 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.155008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.149298 restraints weight = 9967.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.135515 restraints weight = 14632.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135589 restraints weight = 12393.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8124  Z= 0.288
  Angle     :  0.643   7.932  11034  Z= 0.341
  Chirality :  0.042   0.145   1272
  Planarity :  0.004   0.035   1446
  Dihedral  :  5.256  24.088   1089
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.14 %
    Favored  : 96.57 %
  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:  1.17 (0.26), residues: 1020
  helix:  2.93 (0.23), residues: 471
  sheet: -0.10 (0.41), residues: 126
  loop : -1.59 (0.27), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1206 
 HIS   0.007   0.002   HIS A1114 
 PHE   0.018   0.002   PHE B1092 
 TYR   0.014   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
  108 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1183 LYS cc_start: 0.7751 (tttt) cc_final: 0.7514 (tttm)
REVERT: A 1237 ARG cc_start: 0.7107 (mmp80) cc_final: 0.6495 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7424 (tt0) cc_final: 0.6955 (tt0)
REVERT: B 1084 LYS cc_start: 0.8013 (mttt) cc_final: 0.7555 (mttt)
REVERT: C 1092 PHE cc_start: 0.8514 (t80) cc_final: 0.7995 (t80)
REVERT: C 1132 CYS cc_start: 0.4270 (t) cc_final: 0.4053 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2294
  time to fit residues: 33.9059
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  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.155441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.149941 restraints weight = 10078.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.137712 restraints weight = 14553.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.137470 restraints weight = 17034.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.5806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8124  Z= 0.300
  Angle     :  0.660   8.258  11034  Z= 0.347
  Chirality :  0.043   0.143   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  5.286  24.365   1089
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.33 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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:  1.01 (0.26), residues: 1020
  helix:  2.68 (0.23), residues: 480
  sheet: -0.30 (0.40), residues: 126
  loop : -1.55 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C1206 
 HIS   0.007   0.002   HIS A1114 
 PHE   0.021   0.002   PHE C 796 
 TYR   0.018   0.002   TYR A1233 
 ARG   0.003   0.001   ARG C1045 

*********************** 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
  108 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1153 TRP cc_start: 0.7286 (m100) cc_final: 0.6307 (m100)
REVERT: A 1174 MET cc_start: 0.5326 (mmm) cc_final: 0.4816 (mmm)
REVERT: B 1077 GLU cc_start: 0.7397 (tt0) cc_final: 0.6972 (tt0)
REVERT: B 1084 LYS cc_start: 0.8008 (mttt) cc_final: 0.7575 (mttt)
REVERT: C 1092 PHE cc_start: 0.8498 (t80) cc_final: 0.7998 (t80)
REVERT: C 1237 ARG cc_start: 0.6012 (mmp80) cc_final: 0.5801 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2601
  time to fit residues: 38.7587
Evaluate side-chains
  79 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 72 optimal weight:    0.8980
   chunk 85 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    0.3980
   chunk 62 optimal weight:    0.0770
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.157817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.152111 restraints weight = 10013.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.138579 restraints weight = 15534.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.138287 restraints weight = 17013.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7422
moved from start:          0.5935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8124  Z= 0.212
  Angle     :  0.585   7.915  11034  Z= 0.310
  Chirality :  0.040   0.143   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.004  22.630   1089
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.43 %
    Favored  : 96.27 %
  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:  1.23 (0.26), residues: 1020
  helix:  2.97 (0.23), residues: 483
  sheet: -0.34 (0.46), residues: 111
  loop : -1.55 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C1153 
 HIS   0.004   0.001   HIS A1114 
 PHE   0.023   0.002   PHE A1092 
 TYR   0.011   0.001   TYR A1117 
 ARG   0.002   0.001   ARG A1237 

*********************** 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
  113 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1153 TRP cc_start: 0.7350 (m100) cc_final: 0.6306 (m100)
REVERT: A 1237 ARG cc_start: 0.6903 (mmp80) cc_final: 0.6254 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7324 (tt0) cc_final: 0.6842 (tt0)
REVERT: B 1084 LYS cc_start: 0.7919 (mttt) cc_final: 0.7550 (mttt)
REVERT: C 1102 LEU cc_start: 0.7795 (mt) cc_final: 0.7445 (mt)
REVERT: C 1132 CYS cc_start: 0.4200 (t) cc_final: 0.3986 (t)
REVERT: C 1237 ARG cc_start: 0.6331 (mmp80) cc_final: 0.6043 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2151
  time to fit residues: 33.8735
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  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0670
   chunk 41 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.7118

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.156103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150552 restraints weight = 10285.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.137834 restraints weight = 15762.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.137496 restraints weight = 16142.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.6041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8124  Z= 0.287
  Angle     :  0.653  10.652  11034  Z= 0.342
  Chirality :  0.042   0.148   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.200  23.715   1089
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.73 %
    Favored  : 95.98 %
  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:  1.09 (0.26), residues: 1020
  helix:  2.99 (0.23), residues: 471
  sheet: -0.48 (0.46), residues: 111
  loop : -1.63 (0.26), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C1153 
 HIS   0.007   0.002   HIS A1114 
 PHE   0.028   0.002   PHE A1092 
 TYR   0.019   0.002   TYR A1233 
 ARG   0.002   0.001   ARG C1089 

********************** 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
  111 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.890 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1174 MET cc_start: 0.5243 (mmm) cc_final: 0.4605 (mmm)
REVERT: A 1237 ARG cc_start: 0.6669 (mmp80) cc_final: 0.6235 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7298 (tt0) cc_final: 0.7020 (tt0)
REVERT: B 1084 LYS cc_start: 0.7979 (mttt) cc_final: 0.7707 (mttt)
REVERT: C 1092 PHE cc_start: 0.8388 (t80) cc_final: 0.7866 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2066
  time to fit residues: 31.4379
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  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    0.0980
   chunk 18 optimal weight:    1.9990
   chunk 83 optimal weight:    0.2980
   chunk 65 optimal weight:    0.0060
   chunk 30 optimal weight:    0.0010
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.2402

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.161027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.155462 restraints weight = 9757.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.142778 restraints weight = 15510.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.142625 restraints weight = 14832.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.6219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8124  Z= 0.164
  Angle     :  0.556   9.852  11034  Z= 0.290
  Chirality :  0.039   0.139   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  4.668  21.381   1089
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.33 %
    Favored  : 96.37 %
  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 (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:  1.46 (0.27), residues: 1020
  helix:  3.29 (0.23), residues: 477
  sheet: -0.28 (0.48), residues: 111
  loop : -1.52 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B1153 
 HIS   0.003   0.001   HIS C 759 
 PHE   0.029   0.002   PHE A1092 
 TYR   0.010   0.001   TYR C1162 
 ARG   0.004   0.001   ARG A1237 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2447.75 seconds
wall clock time: 44 minutes 30.40 seconds (2670.40 seconds total)