Starting phenix.real_space_refine
on Fri Aug 22 15:38:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qtb_18648/08_2025/8qtb_18648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qtb_18648/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qtb_18648/08_2025/8qtb_18648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qtb_18648/08_2025/8qtb_18648.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qtb_18648/08_2025/8qtb_18648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qtb_18648/08_2025/8qtb_18648.map"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.57, per 1000 atoms: 0.31
  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: 0.41
  Conformation dependent library (CDL) restraints added in 183.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.15
  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: 0.73

  Time building geometry restraints manager: 0.51 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: 0.01
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:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.920
  Find NCS groups from input model:        0.030
  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:8.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.730
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (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
 ARG   0.001   0.000   ARG B1198 
 TYR   0.004   0.000   TYR A1142 
 PHE   0.005   0.001   PHE A 944 
 TRP   0.003   0.000   TRP A1155 
 HIS   0.001   0.000   HIS A1147 

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

*********************** 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  : 0.208 
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: 0.7574
  time to fit residues: 38.2058
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  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.0570
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    3.0106

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.067672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.047376 restraints weight = 15064.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.2701 rms_B_bonded: 4.73
r_work: 0.2526 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5209  Z= 0.272
  Angle     :  0.619   5.854   7110  Z= 0.334
  Chirality :  0.046   0.143    760
  Planarity :  0.004   0.021    934
  Dihedral  :  3.769  11.139    710
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.04 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.32), residues: 658
  helix:  2.22 (0.44), residues: 116
  sheet:  2.53 (0.47), residues: 122
  loop : -0.86 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1050 
 TYR   0.011   0.002   TYR A 911 
 PHE   0.009   0.001   PHE A1135 
 TRP   0.009   0.001   TRP B1155 
 HIS   0.003   0.001   HIS A1109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00608 ( 5180)
  covalent geometry    : angle       0.61506 ( 7052)
  SS BOND              : bond        0.00413 (   29)
  SS BOND              : angle       0.95538 (   58)
  hydrogen bonds       : bond        0.06066 (  188)
  hydrogen bonds       : angle       4.97765 (  504)

*********************** 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
  23 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9349 (mmm) cc_final: 0.8983 (mmp)
REVERT: B 1222 MET cc_start: 0.9358 (mmm) cc_final: 0.8989 (mmp)
  outliers start: 6
  outliers final: 2
  residues processed: 21
  average time/residue: 0.7082
  time to fit residues: 15.5181
Evaluate side-chains
  15 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
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 48 optimal weight:   20.0000
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3243 r_free = 0.3243 target = 0.069015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.048248 restraints weight = 15062.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 4.76
r_work: 0.2544 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.2544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8726
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5209  Z= 0.171
  Angle     :  0.547   7.273   7110  Z= 0.289
  Chirality :  0.044   0.146    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.671  11.892    710
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 11.25 %
    Favored  : 86.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.31), residues: 658
  helix:  2.06 (0.44), residues: 116
  sheet:  2.39 (0.47), residues: 122
  loop : -0.91 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1031 
 TYR   0.008   0.001   TYR A 911 
 PHE   0.007   0.001   PHE A1135 
 TRP   0.003   0.001   TRP B1155 
 HIS   0.002   0.001   HIS A1109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5180)
  covalent geometry    : angle       0.54460 ( 7052)
  SS BOND              : bond        0.00313 (   29)
  SS BOND              : angle       0.76199 (   58)
  hydrogen bonds       : bond        0.04961 (  188)
  hydrogen bonds       : angle       4.55551 (  504)

*********************** 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
  31 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 16
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9406 (mmm) cc_final: 0.9010 (mmp)
REVERT: B 1222 MET cc_start: 0.9402 (mmm) cc_final: 0.9008 (mmp)
  outliers start: 15
  outliers final: 3
  residues processed: 29
  average time/residue: 0.5001
  time to fit residues: 15.2530
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1012 LEU
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 20 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0670
   chunk 22 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 63 optimal weight:    0.1980
   overall best weight:    1.2322

-------------------------------------------------------------------------------
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 = 0.3258 r_free = 0.3258 target = 0.069743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.048974 restraints weight = 15101.089|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 4.74
r_work: 0.2562 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8718
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5209  Z= 0.134
  Angle     :  0.533   7.568   7110  Z= 0.277
  Chirality :  0.044   0.153    760
  Planarity :  0.003   0.023    934
  Dihedral  :  3.551  11.879    710
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 11.43 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.32), residues: 658
  helix:  2.07 (0.43), residues: 116
  sheet:  2.22 (0.46), residues: 122
  loop : -0.90 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1031 
 TYR   0.006   0.001   TYR B1142 
 PHE   0.007   0.001   PHE B1135 
 TRP   0.002   0.000   TRP B1014 
 HIS   0.001   0.000   HIS A 933 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5180)
  covalent geometry    : angle       0.53159 ( 7052)
  SS BOND              : bond        0.00271 (   29)
  SS BOND              : angle       0.71013 (   58)
  hydrogen bonds       : bond        0.04373 (  188)
  hydrogen bonds       : angle       4.24844 (  504)

*********************** 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
  34 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 17
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1186 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8401 (pt)
REVERT: A 1187 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7008 (mtp-110)
REVERT: A 1222 MET cc_start: 0.9411 (mmm) cc_final: 0.9030 (mmp)
REVERT: B 1222 MET cc_start: 0.9402 (mmm) cc_final: 0.9032 (mmp)
  outliers start: 17
  outliers final: 6
  residues processed: 32
  average time/residue: 0.5553
  time to fit residues: 18.5327
Evaluate side-chains
  25 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 17
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1012 LEU
Chi-restraints excluded: chain A residue 1151 LEU
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 1012 LEU
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 10 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.9786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.068259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.047471 restraints weight = 15359.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2696 rms_B_bonded: 4.79
r_work: 0.2522 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5209  Z= 0.186
  Angle     :  0.553   7.595   7110  Z= 0.291
  Chirality :  0.044   0.155    760
  Planarity :  0.003   0.023    934
  Dihedral  :  3.711  11.319    710
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.68 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.32), residues: 658
  helix:  2.02 (0.44), residues: 116
  sheet:  2.16 (0.46), residues: 122
  loop : -0.99 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B1198 
 TYR   0.007   0.001   TYR B1142 
 PHE   0.007   0.001   PHE A1135 
 TRP   0.004   0.001   TRP B1155 
 HIS   0.002   0.001   HIS B1109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 5180)
  covalent geometry    : angle       0.55081 ( 7052)
  SS BOND              : bond        0.00331 (   29)
  SS BOND              : angle       0.77790 (   58)
  hydrogen bonds       : bond        0.05013 (  188)
  hydrogen bonds       : angle       4.38866 (  504)

*********************** 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
  26 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1186 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8517 (pt)
REVERT: A 1187 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6957 (mtp-110)
REVERT: A 1222 MET cc_start: 0.9400 (mmm) cc_final: 0.9021 (mmp)
REVERT: B 1222 MET cc_start: 0.9394 (mmm) cc_final: 0.9019 (mmp)
  outliers start: 10
  outliers final: 4
  residues processed: 25
  average time/residue: 0.6213
  time to fit residues: 16.2887
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  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain A residue 1151 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0470
   chunk 1 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    1.6682

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

Flipped N/Q/H residues before XYZ refinement:
** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.068324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.047807 restraints weight = 15042.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.2711 rms_B_bonded: 4.70
r_work: 0.2536 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5209  Z= 0.161
  Angle     :  0.550   8.324   7110  Z= 0.287
  Chirality :  0.044   0.155    760
  Planarity :  0.003   0.024    934
  Dihedral  :  3.676  11.416    710
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.86 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.31), residues: 658
  helix:  1.95 (0.43), residues: 116
  sheet:  2.03 (0.46), residues: 122
  loop : -1.01 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1031 
 TYR   0.007   0.001   TYR B1142 
 PHE   0.007   0.001   PHE B1135 
 TRP   0.003   0.001   TRP B1014 
 HIS   0.002   0.001   HIS B1107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 5180)
  covalent geometry    : angle       0.54859 ( 7052)
  SS BOND              : bond        0.00292 (   29)
  SS BOND              : angle       0.74148 (   58)
  hydrogen bonds       : bond        0.04650 (  188)
  hydrogen bonds       : angle       4.24607 (  504)

*********************** 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
  25 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 16
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1187 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6995 (mtp-110)
REVERT: A 1222 MET cc_start: 0.9404 (mmm) cc_final: 0.9031 (mmp)
REVERT: B  926 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8524 (mm-30)
REVERT: B 1222 MET cc_start: 0.9397 (mmm) cc_final: 0.9023 (mmp)
  outliers start: 9
  outliers final: 3
  residues processed: 25
  average time/residue: 0.7195
  time to fit residues: 18.7050
Evaluate side-chains
  20 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 16
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0670
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.070081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.049307 restraints weight = 14956.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 4.75
r_work: 0.2575 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5209  Z= 0.110
  Angle     :  0.549  10.043   7110  Z= 0.280
  Chirality :  0.044   0.153    760
  Planarity :  0.003   0.023    934
  Dihedral  :  3.498  11.959    710
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.57 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.32), residues: 658
  helix:  1.96 (0.43), residues: 116
  sheet:  1.91 (0.45), residues: 122
  loop : -0.96 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1031 
 TYR   0.005   0.001   TYR B1142 
 PHE   0.006   0.001   PHE B1135 
 TRP   0.003   0.000   TRP B1014 
 HIS   0.002   0.000   HIS B1107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 5180)
  covalent geometry    : angle       0.54840 ( 7052)
  SS BOND              : bond        0.00242 (   29)
  SS BOND              : angle       0.66578 (   58)
  hydrogen bonds       : bond        0.03802 (  188)
  hydrogen bonds       : angle       3.99576 (  504)

*********************** 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
  22 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 14
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9410 (mmm) cc_final: 0.9029 (mmp)
REVERT: B 1222 MET cc_start: 0.9399 (mmm) cc_final: 0.9017 (mmp)
  outliers start: 8
  outliers final: 3
  residues processed: 22
  average time/residue: 0.7654
  time to fit residues: 17.5581
Evaluate side-chains
  17 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 14
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain B residue  941 GLN
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 20 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0980
   chunk 41 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0370
   chunk 35 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 15 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.070833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.050021 restraints weight = 15017.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 4.74
r_work: 0.2591 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5209  Z= 0.109
  Angle     :  0.570  10.605   7110  Z= 0.287
  Chirality :  0.044   0.153    760
  Planarity :  0.003   0.023    934
  Dihedral  :  3.463  12.137    710
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 14.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.31), residues: 658
  helix:  1.89 (0.43), residues: 116
  sheet:  1.91 (0.45), residues: 122
  loop : -0.97 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1193 
 TYR   0.005   0.001   TYR B1142 
 PHE   0.005   0.001   PHE B1135 
 TRP   0.003   0.000   TRP B1155 
 HIS   0.002   0.000   HIS B1107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5180)
  covalent geometry    : angle       0.56875 ( 7052)
  SS BOND              : bond        0.00253 (   29)
  SS BOND              : angle       0.72122 (   58)
  hydrogen bonds       : bond        0.03677 (  188)
  hydrogen bonds       : angle       3.87216 (  504)

*********************** 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
  18 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 14
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1222 MET cc_start: 0.9397 (mmm) cc_final: 0.9031 (mmp)
REVERT: B 1222 MET cc_start: 0.9389 (mmm) cc_final: 0.9007 (mmp)
  outliers start: 4
  outliers final: 2
  residues processed: 18
  average time/residue: 0.7033
  time to fit residues: 13.2604
Evaluate side-chains
  16 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain B residue  941 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 14 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 52 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.070536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.049524 restraints weight = 15023.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 4.79
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5209  Z= 0.112
  Angle     :  0.560  10.531   7110  Z= 0.283
  Chirality :  0.044   0.154    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.413  11.652    710
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 14.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.32), residues: 658
  helix:  2.00 (0.43), residues: 116
  sheet:  1.81 (0.44), residues: 126
  loop : -0.93 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1187 
 TYR   0.006   0.001   TYR B1142 
 PHE   0.005   0.001   PHE B1135 
 TRP   0.003   0.000   TRP B1014 
 HIS   0.002   0.000   HIS B1107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5180)
  covalent geometry    : angle       0.55950 ( 7052)
  SS BOND              : bond        0.00239 (   29)
  SS BOND              : angle       0.64119 (   58)
  hydrogen bonds       : bond        0.03709 (  188)
  hydrogen bonds       : angle       3.89869 (  504)

*********************** 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
  21 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 15
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1148 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8883 (pp20)
REVERT: A 1222 MET cc_start: 0.9330 (mmm) cc_final: 0.9021 (mmp)
REVERT: B 1222 MET cc_start: 0.9311 (mmm) cc_final: 0.8994 (mmp)
  outliers start: 6
  outliers final: 2
  residues processed: 21
  average time/residue: 0.6763
  time to fit residues: 14.8602
Evaluate side-chains
  16 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain B residue  941 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 42 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.069852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.048960 restraints weight = 15081.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.2742 rms_B_bonded: 4.78
r_work: 0.2567 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5209  Z= 0.135
  Angle     :  0.576  11.130   7110  Z= 0.293
  Chirality :  0.044   0.170    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.511  13.860    710
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 14.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.28 (0.31), residues: 658
  helix:  1.95 (0.43), residues: 116
  sheet:  1.94 (0.45), residues: 122
  loop : -0.94 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1187 
 TYR   0.007   0.001   TYR B1142 
 PHE   0.006   0.001   PHE B1135 
 TRP   0.003   0.000   TRP A1014 
 HIS   0.002   0.000   HIS B1107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5180)
  covalent geometry    : angle       0.57464 ( 7052)
  SS BOND              : bond        0.00283 (   29)
  SS BOND              : angle       0.73111 (   58)
  hydrogen bonds       : bond        0.04111 (  188)
  hydrogen bonds       : angle       3.93344 (  504)

********************** 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
  16 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1148 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9018 (pp20)
REVERT: A 1222 MET cc_start: 0.9361 (mmm) cc_final: 0.8980 (mmp)
REVERT: B 1148 GLU cc_start: 0.9386 (tm-30) cc_final: 0.9100 (pp20)
REVERT: B 1222 MET cc_start: 0.9353 (mmm) cc_final: 0.8970 (mmp)
  outliers start: 2
  outliers final: 2
  residues processed: 16
  average time/residue: 0.8170
  time to fit residues: 13.6002
Evaluate side-chains
  16 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 14
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  941 GLN
Chi-restraints excluded: chain B residue  941 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 36 optimal weight:    0.4980
   chunk 8 optimal weight:    6.9990
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B1107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.070207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.049134 restraints weight = 15211.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.2748 rms_B_bonded: 4.84
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5209  Z= 0.121
  Angle     :  0.566  11.223   7110  Z= 0.287
  Chirality :  0.044   0.174    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.491  14.039    710
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  : 14.82 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.32), residues: 658
  helix:  1.98 (0.43), residues: 116
  sheet:  1.94 (0.45), residues: 122
  loop : -0.92 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1187 
 TYR   0.006   0.001   TYR B1142 
 PHE   0.006   0.001   PHE B1135 
 TRP   0.003   0.000   TRP A1014 
 HIS   0.002   0.000   HIS B1107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 5180)
  covalent geometry    : angle       0.56552 ( 7052)
  SS BOND              : bond        0.00250 (   29)
  SS BOND              : angle       0.64807 (   58)
  hydrogen bonds       : bond        0.03837 (  188)
  hydrogen bonds       : angle       3.94500 (  504)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1246.11 seconds
wall clock time: 22 minutes 3.90 seconds (1323.90 seconds total)