Starting phenix.real_space_refine
on Sat May 10 04:57:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qtb_18648/05_2025/8qtb_18648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qtb_18648/05_2025/8qtb_18648.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qtb_18648/05_2025/8qtb_18648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qtb_18648/05_2025/8qtb_18648.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qtb_18648/05_2025/8qtb_18648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qtb_18648/05_2025/8qtb_18648.cif"
  }
  resolution = 2.94
  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=   0.012
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: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      66      5.16       5
     C    3160      2.51       5
     N     850      2.21       5
     O     972      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5050
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2524
          Classifications: {'peptide': 331}
          Link IDs: {'PTRANS': 21, 'TRANS': 309}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.43, per 1000 atoms: 0.88
  Number of scatterers: 5050
  At special positions: 0
  Unit cell: (102.34, 86.86, 76.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      66     16.00
     O     972      8.00
     N     850      7.00
     C    3160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=29, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 903 " - pdb=" SG  CYS A1036 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 925 " - pdb=" SG  CYS A1071 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 934 " - pdb=" SG  CYS A1033 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 953 " - pdb=" SG  CYS A 960 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1081 " - pdb=" SG  CYS A1124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1095 " - pdb=" SG  CYS A1119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1106 " - pdb=" SG  CYS A1146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1126 " - pdb=" SG  CYS A1134 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A1136 " - pdb=" SG  CYS A1161 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1152 " - pdb=" SG  CYS A1181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1165 " - pdb=" SG  CYS A1206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1174 " - pdb=" SG  CYS B1174 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1185 " - pdb=" SG  CYS A1196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1189 " - pdb=" SG  CYS A1228 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1210 " - pdb=" SG  CYS A1224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 903 " - pdb=" SG  CYS B1036 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 925 " - pdb=" SG  CYS B1071 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 934 " - pdb=" SG  CYS B1033 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 953 " - pdb=" SG  CYS B 960 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1081 " - pdb=" SG  CYS B1124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1095 " - pdb=" SG  CYS B1119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1106 " - pdb=" SG  CYS B1146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1126 " - pdb=" SG  CYS B1134 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B1136 " - pdb=" SG  CYS B1161 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1152 " - pdb=" SG  CYS B1181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1165 " - pdb=" SG  CYS B1206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1185 " - pdb=" SG  CYS B1196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1189 " - pdb=" SG  CYS B1228 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1210 " - pdb=" SG  CYS B1224 " 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: 1.18
  Conformation dependent library (CDL) restraints added in 611.7 milliseconds
  

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1212

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 6 sheets defined
      25.4% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1026 through 1029
    Processing helix  chain 'A' and resid 1057 through 1064
    Processing helix  chain 'A' and resid 1079 through 1084
    Processing helix  chain 'A' and resid 1087 through 1096
    Processing helix  chain 'A' and resid 1097 through 1102
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1103 through 1110
      removed outlier: 4.032A  pdb=" N   ALA A1108 " --> pdb=" O   ALA A1104 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   HIS A1109 " --> pdb=" O   ALA A1105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1126
    Processing helix  chain 'A' and resid 1130 through 1150
      removed outlier: 3.856A  pdb=" N   VAL A1149 " --> pdb=" O   ALA A1145 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLY A1150 " --> pdb=" O   CYS A1146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1169
    Processing helix  chain 'B' and resid 1026 through 1029
    Processing helix  chain 'B' and resid 1057 through 1064
    Processing helix  chain 'B' and resid 1079 through 1084
    Processing helix  chain 'B' and resid 1087 through 1096
    Processing helix  chain 'B' and resid 1097 through 1102
      Proline residue:  B1101  - end of helix
    Processing helix  chain 'B' and resid 1103 through 1110
      removed outlier: 4.034A  pdb=" N   ALA B1108 " --> pdb=" O   ALA B1104 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   HIS B1109 " --> pdb=" O   ALA B1105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1112 through 1126
    Processing helix  chain 'B' and resid 1130 through 1150
      removed outlier: 3.856A  pdb=" N   VAL B1149 " --> pdb=" O   ALA B1145 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLY B1150 " --> pdb=" O   CYS B1146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1164 through 1169
    Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920
      removed outlier: 4.038A  pdb=" N   LEU A1010 " --> pdb=" O   THR A1006 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 979 through 984
      removed outlier: 5.954A  pdb=" N   GLU A 972 " --> pdb=" O   ILE A 983 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   SER A 961 " --> pdb=" O   VAL A 951 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   VAL A 951 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA A 963 " --> pdb=" O   GLU A 949 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   PHE A 944 " --> pdb=" O   GLN A 931 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   GLN A 931 " --> pdb=" O   PHE A 944 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL A 946 " --> pdb=" O   LEU A 929 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1179
      removed outlier: 3.784A  pdb=" N   GLY A1205 " --> pdb=" O   GLN A1179 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 918 through 920
      removed outlier: 4.039A  pdb=" N   LEU B1010 " --> pdb=" O   THR B1006 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 979 through 984
      removed outlier: 5.954A  pdb=" N   GLU B 972 " --> pdb=" O   ILE B 983 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   SER B 961 " --> pdb=" O   VAL B 951 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   VAL B 951 " --> pdb=" O   SER B 961 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ALA B 963 " --> pdb=" O   GLU B 949 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   PHE B 944 " --> pdb=" O   GLN B 931 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   GLN B 931 " --> pdb=" O   PHE B 944 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL B 946 " --> pdb=" O   LEU B 929 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1176 through 1179
      removed outlier: 3.784A  pdb=" N   GLY B1205 " --> pdb=" O   GLN B1179 " (cutoff:3.500A)

    188 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1678
        1.34 -     1.46: 1200
        1.46 -     1.58: 2232
        1.58 -     1.70: 0
        1.70 -     1.82: 70
  Bond restraints: 5180
  Sorted by residual:
  bond pdb=" N   THR B 940 "
       pdb=" CA  THR B 940 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.012 1.54e-02 4.22e+03 5.82e-01
  bond pdb=" N   THR A 940 "
       pdb=" CA  THR A 940 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.54e-02 4.22e+03 5.54e-01
  bond pdb=" CA  THR B 940 "
       pdb=" CB  THR B 940 "
    ideal  model  delta    sigma   weight residual
    1.527  1.539 -0.012 1.70e-02 3.46e+03 4.78e-01
  bond pdb=" CA  THR A 940 "
       pdb=" CB  THR A 940 "
    ideal  model  delta    sigma   weight residual
    1.527  1.538 -0.011 1.70e-02 3.46e+03 4.09e-01
  bond pdb=" C   ALA B1138 "
       pdb=" O   ALA B1138 "
    ideal  model  delta    sigma   weight residual
    1.236  1.243 -0.006 1.15e-02 7.56e+03 2.94e-01
  ... (remaining 5175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.79: 6777
        0.79 -     1.59: 209
        1.59 -     2.38: 29
        2.38 -     3.17: 29
        3.17 -     3.96: 8
  Bond angle restraints: 7052
  Sorted by residual:
  angle pdb=" C   SER A 939 "
        pdb=" N   THR A 940 "
        pdb=" CA  THR A 940 "
      ideal   model   delta    sigma   weight residual
     122.46  125.30   -2.84 1.41e+00 5.03e-01 4.06e+00
  angle pdb=" C   SER B 939 "
        pdb=" N   THR B 940 "
        pdb=" CA  THR B 940 "
      ideal   model   delta    sigma   weight residual
     122.46  125.27   -2.81 1.41e+00 5.03e-01 3.96e+00
  angle pdb=" C   LYS A1016 "
        pdb=" N   LYS A1017 "
        pdb=" CA  LYS A1017 "
      ideal   model   delta    sigma   weight residual
     122.56  120.51    2.05 1.50e+00 4.44e-01 1.86e+00
  angle pdb=" CA  THR A 940 "
        pdb=" CB  THR A 940 "
        pdb=" CG2 THR A 940 "
      ideal   model   delta    sigma   weight residual
     110.50  112.81   -2.31 1.70e+00 3.46e-01 1.84e+00
  angle pdb=" CA  THR B 940 "
        pdb=" CB  THR B 940 "
        pdb=" CG2 THR B 940 "
      ideal   model   delta    sigma   weight residual
     110.50  112.78   -2.28 1.70e+00 3.46e-01 1.80e+00
  ... (remaining 7047 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 2898
       17.41 -    34.83: 209
       34.83 -    52.24: 34
       52.24 -    69.66: 6
       69.66 -    87.07: 2
  Dihedral angle restraints: 3149
    sinusoidal: 1251
      harmonic: 1898
  Sorted by residual:
  dihedral pdb=" CB  CYS A 953 "
           pdb=" SG  CYS A 953 "
           pdb=" SG  CYS A 960 "
           pdb=" CB  CYS A 960 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.93  -87.07     1      1.00e+01 1.00e-02 9.11e+01
  dihedral pdb=" CB  CYS B 953 "
           pdb=" SG  CYS B 953 "
           pdb=" SG  CYS B 960 "
           pdb=" CB  CYS B 960 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.93  -87.07     1      1.00e+01 1.00e-02 9.11e+01
  dihedral pdb=" CB  CYS A1185 "
           pdb=" SG  CYS A1185 "
           pdb=" SG  CYS A1196 "
           pdb=" CB  CYS A1196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.71   53.29     1      1.00e+01 1.00e-02 3.86e+01
  ... (remaining 3146 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 432
       0.024 -    0.047: 187
       0.047 -    0.071: 58
       0.071 -    0.095: 33
       0.095 -    0.118: 50
  Chirality restraints: 760
  Sorted by residual:
  chirality pdb=" CA  VAL B 905 "
            pdb=" N   VAL B 905 "
            pdb=" C   VAL B 905 "
            pdb=" CB  VAL B 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.51e-01
  chirality pdb=" CA  VAL A 905 "
            pdb=" N   VAL A 905 "
            pdb=" C   VAL A 905 "
            pdb=" CB  VAL A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  ILE A 964 "
            pdb=" N   ILE A 964 "
            pdb=" C   ILE A 964 "
            pdb=" CB  ILE A 964 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.38e-01
  ... (remaining 757 not shown)

  Planarity restraints: 934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A1018 "   -0.005 2.00e-02 2.50e+03   9.70e-03 9.41e-01
        pdb=" C   THR A1018 "    0.017 2.00e-02 2.50e+03
        pdb=" O   THR A1018 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   SER A1019 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B1025 "   -0.016 5.00e-02 4.00e+02   2.40e-02 9.21e-01
        pdb=" N   PRO B1026 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO B1026 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B1026 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1025 "    0.016 5.00e-02 4.00e+02   2.37e-02 9.02e-01
        pdb=" N   PRO A1026 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A1026 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A1026 "    0.013 5.00e-02 4.00e+02
  ... (remaining 931 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1805
        2.85 -     3.36: 4388
        3.36 -     3.88: 8161
        3.88 -     4.39: 8984
        4.39 -     4.90: 15436
  Nonbonded interactions: 38774
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A1079 "
            pdb=" OG1 THR A1082 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OD2 ASP B1079 "
            pdb=" OG1 THR B1082 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OD1 ASP B1040 "
            pdb="CA    CA B1501 "
     model   vdw
     2.350 2.510
  nonbonded pdb=" OD1 ASP A1040 "
            pdb="CA    CA A1501 "
     model   vdw
     2.350 2.510
  nonbonded pdb=" OD1 ASP A1046 "
            pdb="CA    CA A1501 "
     model   vdw
     2.353 2.510
  ... (remaining 38769 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.430
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.590
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
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      :  0.002   0.016   5209  Z= 0.077
  Angle     :  0.390   3.963   7110  Z= 0.204
  Chirality :  0.041   0.118    760
  Planarity :  0.003   0.024    934
  Dihedral  : 11.054  55.271   1850
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  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:  0.70 (0.32), residues: 658
  helix:  2.40 (0.43), residues: 114
  sheet:  2.78 (0.48), residues: 104
  loop : -0.71 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A1155 
 HIS   0.001   0.000   HIS A1147 
 PHE   0.005   0.001   PHE A 944 
 TYR   0.004   0.000   TYR A1142 
 ARG   0.001   0.000   ARG B1198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21085 (  188)
  hydrogen bonds       : angle       7.03719 (  504)
  SS BOND              : bond        0.00178 (   29)
  SS BOND              : angle       0.47465 (   58)
  covalent geometry    : bond        0.00156 ( 5180)
  covalent geometry    : angle       0.38973 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  979 LYS cc_start: 0.9250 (ptpt) cc_final: 0.8908 (mtmm)
REVERT: A  998 MET cc_start: 0.9340 (mtp) cc_final: 0.9005 (mtt)
REVERT: A 1222 MET cc_start: 0.9257 (mmm) cc_final: 0.8975 (mmp)
REVERT: B  979 LYS cc_start: 0.9249 (ptpt) cc_final: 0.8883 (mtmm)
REVERT: B  998 MET cc_start: 0.9341 (mtp) cc_final: 0.9016 (mtt)
REVERT: B 1186 LEU cc_start: 0.8520 (tp) cc_final: 0.8259 (pt)
REVERT: B 1222 MET cc_start: 0.9272 (mmm) cc_final: 0.8994 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 1.6221
  time to fit residues: 82.4480
Evaluate side-chains
  23 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0040
   overall best weight:    1.5998

-------------------------------------------------------------------------------
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 = 0.3273 r_free = 0.3273 target = 0.070247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.049514 restraints weight = 14914.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 4.79
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8591
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5209  Z= 0.167
  Angle     :  0.565   6.412   7110  Z= 0.301
  Chirality :  0.044   0.140    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.381  11.361    710
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.68 %
    Favored  : 85.71 %
  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:  0.74 (0.32), residues: 658
  helix:  2.33 (0.43), residues: 116
  sheet:  2.68 (0.48), residues: 122
  loop : -0.79 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B1155 
 HIS   0.002   0.001   HIS B 933 
 PHE   0.007   0.001   PHE A1135 
 TYR   0.009   0.001   TYR B 911 
 ARG   0.003   0.000   ARG A1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05022 (  188)
  hydrogen bonds       : angle       4.84412 (  504)
  SS BOND              : bond        0.00292 (   29)
  SS BOND              : angle       0.79437 (   58)
  covalent geometry    : bond        0.00375 ( 5180)
  covalent geometry    : angle       0.56232 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 23
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9316 (mmm) cc_final: 0.9024 (mmp)
REVERT: B 1186 LEU cc_start: 0.8579 (tp) cc_final: 0.8292 (pt)
REVERT: B 1222 MET cc_start: 0.9327 (mmm) cc_final: 0.9024 (mmp)
  outliers start: 9
  outliers final: 2
  residues processed: 30
  average time/residue: 1.5068
  time to fit residues: 47.3705
Evaluate side-chains
  18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 16
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain B residue 1012 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 11 optimal weight:    0.3980
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3300 r_free = 0.3300 target = 0.071545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.050645 restraints weight = 15017.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 4.79
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5209  Z= 0.109
  Angle     :  0.523   7.507   7110  Z= 0.272
  Chirality :  0.044   0.153    760
  Planarity :  0.003   0.023    934
  Dihedral  :  3.299  11.944    710
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 11.43 %
    Favored  : 85.36 %
  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:  0.59 (0.32), residues: 658
  helix:  2.25 (0.42), residues: 116
  sheet:  2.47 (0.47), residues: 122
  loop : -0.86 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B1014 
 HIS   0.001   0.000   HIS A1147 
 PHE   0.006   0.001   PHE A1135 
 TYR   0.025   0.001   TYR B 993 
 ARG   0.002   0.000   ARG A1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03941 (  188)
  hydrogen bonds       : angle       4.35196 (  504)
  SS BOND              : bond        0.00237 (   29)
  SS BOND              : angle       0.65008 (   58)
  covalent geometry    : bond        0.00242 ( 5180)
  covalent geometry    : angle       0.52177 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 19
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9358 (mmm) cc_final: 0.9034 (mmp)
REVERT: B 1186 LEU cc_start: 0.8631 (tp) cc_final: 0.8255 (pt)
REVERT: B 1222 MET cc_start: 0.9342 (mmm) cc_final: 0.9034 (mmp)
  outliers start: 18
  outliers final: 6
  residues processed: 36
  average time/residue: 0.9555
  time to fit residues: 36.7264
Evaluate side-chains
  22 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 16
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  995 ILE
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain B residue  995 ILE
Chi-restraints excluded: chain B residue 1012 LEU
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 54 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   chunk 48 optimal weight:   20.0000
   chunk 52 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0000
   overall best weight:    0.7986

-------------------------------------------------------------------------------
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 = 0.3290 r_free = 0.3290 target = 0.071023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.050641 restraints weight = 14984.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2791 rms_B_bonded: 4.74
r_work: 0.2619 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5209  Z= 0.110
  Angle     :  0.516   6.677   7110  Z= 0.269
  Chirality :  0.043   0.153    760
  Planarity :  0.003   0.024    934
  Dihedral  :  3.308  11.857    710
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.39 %
    Favored  : 84.82 %
  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:  0.54 (0.32), residues: 658
  helix:  2.26 (0.42), residues: 116
  sheet:  2.34 (0.46), residues: 122
  loop : -0.89 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B1014 
 HIS   0.001   0.000   HIS A1109 
 PHE   0.005   0.001   PHE A1135 
 TYR   0.006   0.001   TYR B1142 
 ARG   0.002   0.000   ARG B1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  188)
  hydrogen bonds       : angle       4.14018 (  504)
  SS BOND              : bond        0.00235 (   29)
  SS BOND              : angle       0.64421 (   58)
  covalent geometry    : bond        0.00245 ( 5180)
  covalent geometry    : angle       0.51450 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 17
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1186 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8238 (mm)
REVERT: A 1187 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6856 (mtp-110)
REVERT: A 1222 MET cc_start: 0.9368 (mmm) cc_final: 0.8994 (mmp)
REVERT: B 1222 MET cc_start: 0.9362 (mmm) cc_final: 0.9000 (mmp)
  outliers start: 10
  outliers final: 4
  residues processed: 25
  average time/residue: 1.3859
  time to fit residues: 36.5602
Evaluate side-chains
  24 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain A residue 1187 ARG
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 65 optimal weight:    0.2980
   chunk 5 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0970
   chunk 59 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3284 r_free = 0.3284 target = 0.070669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.050137 restraints weight = 14656.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.2785 rms_B_bonded: 4.70
r_work: 0.2613 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5209  Z= 0.113
  Angle     :  0.525   7.487   7110  Z= 0.269
  Chirality :  0.043   0.153    760
  Planarity :  0.003   0.023    934
  Dihedral  :  3.328  11.644    710
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 12.86 %
    Favored  : 84.82 %
  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:  0.49 (0.32), residues: 658
  helix:  2.24 (0.42), residues: 116
  sheet:  2.23 (0.45), residues: 122
  loop : -0.90 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A1014 
 HIS   0.001   0.000   HIS B1109 
 PHE   0.006   0.001   PHE A1135 
 TYR   0.006   0.001   TYR B1142 
 ARG   0.001   0.000   ARG A1031 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03838 (  188)
  hydrogen bonds       : angle       4.02801 (  504)
  SS BOND              : bond        0.00240 (   29)
  SS BOND              : angle       0.63632 (   58)
  covalent geometry    : bond        0.00255 ( 5180)
  covalent geometry    : angle       0.52362 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 17
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9386 (mmm) cc_final: 0.9014 (mmp)
REVERT: B 1028 PHE cc_start: 0.9164 (m-80) cc_final: 0.8495 (m-80)
REVERT: B 1222 MET cc_start: 0.9376 (mmm) cc_final: 0.9008 (mmp)
  outliers start: 13
  outliers final: 6
  residues processed: 28
  average time/residue: 1.3089
  time to fit residues: 38.6508
Evaluate side-chains
  21 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1151 LEU
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.070912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.050298 restraints weight = 15025.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 4.74
r_work: 0.2611 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8677
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5209  Z= 0.108
  Angle     :  0.539   8.333   7110  Z= 0.272
  Chirality :  0.044   0.153    760
  Planarity :  0.004   0.055    934
  Dihedral  :  3.344  11.944    710
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.04 %
    Favored  : 84.82 %
  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:  0.46 (0.32), residues: 658
  helix:  2.20 (0.42), residues: 116
  sheet:  2.16 (0.46), residues: 122
  loop : -0.89 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A1014 
 HIS   0.001   0.000   HIS A1109 
 PHE   0.005   0.001   PHE B1135 
 TYR   0.006   0.001   TYR B1142 
 ARG   0.007   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03712 (  188)
  hydrogen bonds       : angle       3.92100 (  504)
  SS BOND              : bond        0.00241 (   29)
  SS BOND              : angle       0.63127 (   58)
  covalent geometry    : bond        0.00244 ( 5180)
  covalent geometry    : angle       0.53810 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 15
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9381 (mmm) cc_final: 0.9015 (mmp)
REVERT: B 1222 MET cc_start: 0.9359 (mmm) cc_final: 0.8996 (mmp)
  outliers start: 12
  outliers final: 7
  residues processed: 26
  average time/residue: 1.5014
  time to fit residues: 41.0101
Evaluate side-chains
  23 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 16
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1050 ARG
Chi-restraints excluded: chain A residue 1183 VAL
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1050 ARG
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 30 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.070824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.050047 restraints weight = 14959.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 4.77
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5209  Z= 0.109
  Angle     :  0.542   8.601   7110  Z= 0.274
  Chirality :  0.044   0.153    760
  Planarity :  0.003   0.036    934
  Dihedral  :  3.320  11.029    710
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.00 %
    Favored  : 83.39 %
  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:  0.43 (0.32), residues: 658
  helix:  2.19 (0.42), residues: 116
  sheet:  1.99 (0.45), residues: 126
  loop : -0.89 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A1014 
 HIS   0.001   0.000   HIS A1109 
 PHE   0.005   0.001   PHE A1135 
 TYR   0.006   0.001   TYR B1142 
 ARG   0.005   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  188)
  hydrogen bonds       : angle       3.87788 (  504)
  SS BOND              : bond        0.00229 (   29)
  SS BOND              : angle       0.62494 (   58)
  covalent geometry    : bond        0.00247 ( 5180)
  covalent geometry    : angle       0.54137 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 16
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9331 (mmm) cc_final: 0.9013 (mmp)
REVERT: B 1222 MET cc_start: 0.9314 (mmm) cc_final: 0.9002 (mmp)
  outliers start: 9
  outliers final: 6
  residues processed: 25
  average time/residue: 1.6083
  time to fit residues: 42.2204
Evaluate side-chains
  21 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1050 ARG
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1050 ARG
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 41 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
A1107 HIS
B1107 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.066954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.046267 restraints weight = 15388.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 4.77
r_work: 0.2493 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   5209  Z= 0.248
  Angle     :  0.620   8.716   7110  Z= 0.327
  Chirality :  0.046   0.158    760
  Planarity :  0.004   0.030    934
  Dihedral  :  3.920  13.700    710
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.46 %
    Favored  : 83.39 %
  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:  0.24 (0.31), residues: 658
  helix:  1.89 (0.44), residues: 116
  sheet:  2.12 (0.47), residues: 122
  loop : -1.03 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1155 
 HIS   0.004   0.001   HIS A1109 
 PHE   0.008   0.001   PHE A1135 
 TYR   0.010   0.001   TYR A 911 
 ARG   0.004   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05819 (  188)
  hydrogen bonds       : angle       4.47894 (  504)
  SS BOND              : bond        0.00403 (   29)
  SS BOND              : angle       0.95267 (   58)
  covalent geometry    : bond        0.00551 ( 5180)
  covalent geometry    : angle       0.61696 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 15
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9357 (mmm) cc_final: 0.8966 (mmp)
REVERT: B 1222 MET cc_start: 0.9353 (mmm) cc_final: 0.8957 (mmp)
  outliers start: 12
  outliers final: 7
  residues processed: 27
  average time/residue: 1.4578
  time to fit residues: 41.3143
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 13
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1050 ARG
Chi-restraints excluded: chain A residue 1151 LEU
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1050 ARG
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0030
   chunk 54 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.5796

-------------------------------------------------------------------------------
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 = 0.3235 r_free = 0.3235 target = 0.068487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.047860 restraints weight = 15055.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2712 rms_B_bonded: 4.72
r_work: 0.2538 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8734
moved from start:          0.2780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5209  Z= 0.158
  Angle     :  0.610  10.620   7110  Z= 0.307
  Chirality :  0.045   0.163    760
  Planarity :  0.004   0.027    934
  Dihedral  :  3.769  13.420    710
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.71 %
    Favored  : 83.21 %
  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:  0.21 (0.31), residues: 658
  helix:  1.92 (0.44), residues: 116
  sheet:  1.87 (0.45), residues: 122
  loop : -0.99 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1155 
 HIS   0.002   0.001   HIS A1109 
 PHE   0.006   0.001   PHE B1135 
 TYR   0.007   0.001   TYR A1142 
 ARG   0.005   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04535 (  188)
  hydrogen bonds       : angle       4.17792 (  504)
  SS BOND              : bond        0.00293 (   29)
  SS BOND              : angle       0.70685 (   58)
  covalent geometry    : bond        0.00356 ( 5180)
  covalent geometry    : angle       0.60937 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9394 (mmm) cc_final: 0.9013 (mmp)
REVERT: B 1222 MET cc_start: 0.9396 (mmm) cc_final: 0.9020 (mmp)
  outliers start: 6
  outliers final: 6
  residues processed: 20
  average time/residue: 1.8248
  time to fit residues: 38.2290
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1050 ARG
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1050 ARG
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3236 r_free = 0.3236 target = 0.068555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.047917 restraints weight = 15042.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 4.73
r_work: 0.2537 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.2537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5209  Z= 0.159
  Angle     :  0.617  10.799   7110  Z= 0.309
  Chirality :  0.045   0.172    760
  Planarity :  0.003   0.025    934
  Dihedral  :  3.737  13.659    710
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 15.71 %
    Favored  : 83.21 %
  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:  0.16 (0.31), residues: 658
  helix:  1.88 (0.43), residues: 116
  sheet:  1.84 (0.45), residues: 122
  loop : -1.02 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1155 
 HIS   0.002   0.001   HIS A1109 
 PHE   0.006   0.001   PHE A1135 
 TYR   0.008   0.001   TYR A1142 
 ARG   0.006   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04554 (  188)
  hydrogen bonds       : angle       4.09623 (  504)
  SS BOND              : bond        0.00301 (   29)
  SS BOND              : angle       0.74152 (   58)
  covalent geometry    : bond        0.00359 ( 5180)
  covalent geometry    : angle       0.61591 ( 7052)

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

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

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1316 Ramachandran restraints generated.
    658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1148 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9111 (pp20)
REVERT: A 1222 MET cc_start: 0.9396 (mmm) cc_final: 0.9019 (mmp)
REVERT: B 1148 GLU cc_start: 0.9396 (tm-30) cc_final: 0.9098 (pp20)
REVERT: B 1222 MET cc_start: 0.9400 (mmm) cc_final: 0.9014 (mmp)
  outliers start: 6
  outliers final: 6
  residues processed: 20
  average time/residue: 1.6901
  time to fit residues: 35.5097
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 14
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1019 SER
Chi-restraints excluded: chain A residue 1050 ARG
Chi-restraints excluded: chain B residue  941 GLN
Chi-restraints excluded: chain B residue 1050 ARG
Chi-restraints excluded: chain B residue 1183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.3253 r_free = 0.3253 target = 0.069325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.048550 restraints weight = 15275.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 4.78
r_work: 0.2554 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8717
moved from start:          0.2786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5209  Z= 0.132
  Angle     :  0.602  10.762   7110  Z= 0.298
  Chirality :  0.044   0.168    760
  Planarity :  0.003   0.024    934
  Dihedral  :  3.637  13.306    710
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.54 %
    Favored  : 83.21 %
  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:  0.19 (0.31), residues: 658
  helix:  1.94 (0.43), residues: 116
  sheet:  1.86 (0.45), residues: 122
  loop : -1.01 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A1014 
 HIS   0.001   0.000   HIS B1109 
 PHE   0.006   0.001   PHE A1135 
 TYR   0.007   0.001   TYR A1142 
 ARG   0.006   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04058 (  188)
  hydrogen bonds       : angle       3.99370 (  504)
  SS BOND              : bond        0.00262 (   29)
  SS BOND              : angle       0.64673 (   58)
  covalent geometry    : bond        0.00299 ( 5180)
  covalent geometry    : angle       0.60117 ( 7052)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2775.00 seconds
wall clock time: 49 minutes 28.52 seconds (2968.52 seconds total)