Starting phenix.real_space_refine
on Sat May 10 05:04:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qtv_18654/05_2025/8qtv_18654.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qtv_18654/05_2025/8qtv_18654.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qtv_18654/05_2025/8qtv_18654.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qtv_18654/05_2025/8qtv_18654.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qtv_18654/05_2025/8qtv_18654.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qtv_18654/05_2025/8qtv_18654.cif"
  }
  resolution = 3.25
  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    3162      2.51       5
     N     854      2.21       5
     O     970      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5054
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 331, 2526
          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: 4.45, per 1000 atoms: 0.88
  Number of scatterers: 5054
  At special positions: 0
  Unit cell: (64.6275, 114.606, 74.9679, 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     970      8.00
     N     854      7.00
     C    3162      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=2.03
    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=2.03
    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: 1.24
  Conformation dependent library (CDL) restraints added in 684.0 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:
      16 helices and 8 sheets defined
      23.0% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  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 1108
      removed outlier: 3.691A  pdb=" N   ALA A1108 " --> pdb=" O   ALA A1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1126
    Processing helix  chain 'A' and resid 1130 through 1150
      removed outlier: 3.598A  pdb=" N   CYS A1134 " --> pdb=" O   GLY A1130 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TYR A1142 " --> pdb=" O   ALA A1138 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A1149 " --> pdb=" O   ALA A1145 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   GLY A1150 " --> pdb=" O   CYS A1146 " (cutoff:3.500A)
    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 1108
      removed outlier: 3.690A  pdb=" N   ALA B1108 " --> pdb=" O   ALA B1104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1112 through 1126
    Processing helix  chain 'B' and resid 1130 through 1150
      removed outlier: 3.598A  pdb=" N   CYS B1134 " --> pdb=" O   GLY B1130 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   TYR B1142 " --> pdb=" O   ALA B1138 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL B1149 " --> pdb=" O   ALA B1145 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY B1150 " --> pdb=" O   CYS B1146 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 918 through 920
      removed outlier: 4.333A  pdb=" N   ALA A 901 " --> pdb=" O   LEU A1024 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A1024 " --> pdb=" O   ALA A 901 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU A1010 " --> pdb=" O   THR A1006 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TRP A1014 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET A 998 " --> pdb=" O   TYR A1001 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 979 through 982
      removed outlier: 3.515A  pdb=" N   ILE A 964 " --> pdb=" O   LEU A 975 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLU A 949 " --> pdb=" O   LYS A 962 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   ILE A 964 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL A 947 " --> pdb=" O   ILE A 964 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   ILE A 966 " --> pdb=" O   ARG A 945 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG A 945 " --> pdb=" O   ILE A 966 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   PHE A 944 " --> pdb=" O   ASN A 932 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 930 " --> pdb=" O   VAL A 946 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR A 948 " --> pdb=" O   THR A 928 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   THR A 928 " --> pdb=" O   THR A 948 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   ASN A 950 " --> pdb=" O   GLU A 926 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   GLU A 926 " --> pdb=" O   ASN A 950 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS A1033 " --> pdb=" O   GLN A 931 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1176 through 1179
      removed outlier: 3.829A  pdb=" N   GLY A1205 " --> pdb=" O   GLN A1179 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1217
    Processing sheet with id=AA5, first strand: chain 'B' and resid 918 through 920
      removed outlier: 4.333A  pdb=" N   ALA B 901 " --> pdb=" O   LEU B1024 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU B1024 " --> pdb=" O   ALA B 901 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LEU B1010 " --> pdb=" O   THR B1006 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   TRP B1014 " --> pdb=" O   LEU B1002 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   MET B 998 " --> pdb=" O   TYR B1001 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 979 through 982
      removed outlier: 3.515A  pdb=" N   ILE B 964 " --> pdb=" O   LEU B 975 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   GLU B 949 " --> pdb=" O   LYS B 962 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   ILE B 964 " --> pdb=" O   VAL B 947 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   VAL B 947 " --> pdb=" O   ILE B 964 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   ILE B 966 " --> pdb=" O   ARG B 945 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ARG B 945 " --> pdb=" O   ILE B 966 " (cutoff:3.500A)
      removed outlier: 5.143A  pdb=" N   PHE B 944 " --> pdb=" O   ASN B 932 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 930 " --> pdb=" O   VAL B 946 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR B 948 " --> pdb=" O   THR B 928 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   THR B 928 " --> pdb=" O   THR B 948 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   ASN B 950 " --> pdb=" O   GLU B 926 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   GLU B 926 " --> pdb=" O   ASN B 950 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS B1033 " --> pdb=" O   GLN B 931 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1176 through 1179
      removed outlier: 3.828A  pdb=" N   GLY B1205 " --> pdb=" O   GLN B1179 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1216 through 1217

    164 hydrogen bonds defined for protein.
    444 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: 1.45

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1680
        1.35 -     1.46: 1224
        1.46 -     1.58: 2210
        1.58 -     1.70: 0
        1.70 -     1.81: 70
  Bond restraints: 5184
  Sorted by residual:
  bond pdb=" N   VAL B1183 "
       pdb=" CA  VAL B1183 "
    ideal  model  delta    sigma   weight residual
    1.468  1.460  0.008 1.05e-02 9.07e+03 5.75e-01
  bond pdb=" CA  GLU A1219 "
       pdb=" CB  GLU A1219 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.69e-02 3.50e+03 5.28e-01
  bond pdb=" CA  GLU B1219 "
       pdb=" CB  GLU B1219 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.69e-02 3.50e+03 5.05e-01
  bond pdb=" N   VAL A1183 "
       pdb=" CA  VAL A1183 "
    ideal  model  delta    sigma   weight residual
    1.468  1.461  0.007 1.05e-02 9.07e+03 4.61e-01
  bond pdb=" CB  PRO B1077 "
       pdb=" CG  PRO B1077 "
    ideal  model  delta    sigma   weight residual
    1.492  1.524 -0.032 5.00e-02 4.00e+02 3.98e-01
  ... (remaining 5179 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 6948
        1.45 -     2.90: 86
        2.90 -     4.35: 18
        4.35 -     5.80: 0
        5.80 -     7.25: 4
  Bond angle restraints: 7056
  Sorted by residual:
  angle pdb=" C   ASP B1218 "
        pdb=" N   GLU B1219 "
        pdb=" CA  GLU B1219 "
      ideal   model   delta    sigma   weight residual
     121.54  127.97   -6.43 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" C   ASP A1218 "
        pdb=" N   GLU A1219 "
        pdb=" CA  GLU A1219 "
      ideal   model   delta    sigma   weight residual
     121.54  127.95   -6.41 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" N   ILE B 983 "
        pdb=" CA  ILE B 983 "
        pdb=" C   ILE B 983 "
      ideal   model   delta    sigma   weight residual
     111.48  109.22    2.26 9.40e-01 1.13e+00 5.80e+00
  angle pdb=" CA  GLY B 954 "
        pdb=" C   GLY B 954 "
        pdb=" N   THR B 955 "
      ideal   model   delta    sigma   weight residual
     114.85  116.83   -1.98 9.50e-01 1.11e+00 4.35e+00
  angle pdb=" CA  GLY A 954 "
        pdb=" C   GLY A 954 "
        pdb=" N   THR A 955 "
      ideal   model   delta    sigma   weight residual
     114.85  116.83   -1.98 9.50e-01 1.11e+00 4.33e+00
  ... (remaining 7051 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 2810
       17.40 -    34.79: 255
       34.79 -    52.19: 78
       52.19 -    69.58: 4
       69.58 -    86.98: 6
  Dihedral angle restraints: 3153
    sinusoidal: 1255
      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
     -86.00 -172.98   86.98     1      1.00e+01 1.00e-02 9.09e+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
     -86.00 -172.94   86.94     1      1.00e+01 1.00e-02 9.09e+01
  dihedral pdb=" CB  CYS A1189 "
           pdb=" SG  CYS A1189 "
           pdb=" SG  CYS A1228 "
           pdb=" CB  CYS A1228 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -155.77   69.77     1      1.00e+01 1.00e-02 6.28e+01
  ... (remaining 3150 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 417
       0.024 -    0.048: 192
       0.048 -    0.072: 67
       0.072 -    0.096: 45
       0.096 -    0.120: 39
  Chirality restraints: 760
  Sorted by residual:
  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 3.57e-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 3.48e-01
  chirality pdb=" CA  ILE A1020 "
            pdb=" N   ILE A1020 "
            pdb=" C   ILE A1020 "
            pdb=" CB  ILE A1020 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.29e-01
  ... (remaining 757 not shown)

  Planarity restraints: 934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B1191 "    0.013 5.00e-02 4.00e+02   2.02e-02 6.52e-01
        pdb=" N   PRO B1192 "   -0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO B1192 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B1192 "    0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1191 "   -0.013 5.00e-02 4.00e+02   1.99e-02 6.36e-01
        pdb=" N   PRO A1192 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A1192 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A1192 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 991 "    0.013 5.00e-02 4.00e+02   1.92e-02 5.89e-01
        pdb=" N   PRO B 992 "   -0.033 5.00e-02 4.00e+02
        pdb=" CA  PRO B 992 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 992 "    0.011 5.00e-02 4.00e+02
  ... (remaining 931 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1585
        2.82 -     3.34: 4393
        3.34 -     3.86: 8145
        3.86 -     4.38: 8746
        4.38 -     4.90: 15250
  Nonbonded interactions: 38119
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP B1079 "
            pdb=" OG1 THR B1082 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OD2 ASP A1079 "
            pdb=" OG1 THR A1082 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   THR A1049 "
            pdb=" OG1 THR A1049 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   THR B1049 "
            pdb=" OG1 THR B1049 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OD2 ASP B1015 "
            pdb=" OG  SER B1019 "
     model   vdw
     2.378 3.040
  ... (remaining 38114 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: 0.03
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:             2.320
  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:          0.460
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     17.070
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
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   0.032   5213  Z= 0.074
  Angle     :  0.428   7.252   7114  Z= 0.216
  Chirality :  0.041   0.120    760
  Planarity :  0.002   0.020    934
  Dihedral  : 13.649  73.393   1854
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.36 %
    Favored  : 84.64 %
  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: -0.99 (0.32), residues: 658
  helix:  0.82 (0.45), residues: 128
  sheet:  0.22 (0.52), residues: 100
  loop : -1.42 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A1090 
 HIS   0.001   0.000   HIS B1147 
 PHE   0.003   0.000   PHE A1135 
 TYR   0.004   0.000   TYR A 906 
 ARG   0.001   0.000   ARG B 996 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22170 (  164)
  hydrogen bonds       : angle       6.10120 (  444)
  SS BOND              : bond        0.00131 (   29)
  SS BOND              : angle       0.37900 (   58)
  covalent geometry    : bond        0.00166 ( 5184)
  covalent geometry    : angle       0.42841 ( 7056)

*********************** 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
  37 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.2169
  time to fit residues: 10.3331
Evaluate side-chains
  27 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 50 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0040
   chunk 51 optimal weight:    0.4980
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.4796

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.071523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.050953 restraints weight = 14569.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 4.88
r_work: 0.2568 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5213  Z= 0.145
  Angle     :  0.516   6.422   7114  Z= 0.266
  Chirality :  0.043   0.125    760
  Planarity :  0.003   0.021    934
  Dihedral  :  3.269  21.439    712
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.54 %
    Favored  : 83.04 %
  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 (0.33), residues: 658
  helix:  1.54 (0.47), residues: 116
  sheet:  0.32 (0.48), residues: 120
  loop : -1.08 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1014 
 HIS   0.002   0.000   HIS B1147 
 PHE   0.005   0.001   PHE B1028 
 TYR   0.006   0.001   TYR A1167 
 ARG   0.008   0.000   ARG B1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  164)
  hydrogen bonds       : angle       4.22647 (  444)
  SS BOND              : bond        0.00251 (   29)
  SS BOND              : angle       0.71481 (   58)
  covalent geometry    : bond        0.00333 ( 5184)
  covalent geometry    : angle       0.51374 ( 7056)

*********************** 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
  34 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  931 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7290 (tm-30)
REVERT: A  942 ASP cc_start: 0.8689 (t0) cc_final: 0.8321 (t0)
REVERT: B  931 GLN cc_start: 0.7197 (tm-30) cc_final: 0.6966 (tm-30)
REVERT: B  942 ASP cc_start: 0.8616 (t0) cc_final: 0.8393 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 32
  average time/residue: 0.1661
  time to fit residues: 7.5545
Evaluate side-chains
  26 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 22
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    0.5980
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.6984

-------------------------------------------------------------------------------
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 = 0.3265 r_free = 0.3265 target = 0.070870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.049855 restraints weight = 14641.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.2710 rms_B_bonded: 5.06
r_work: 0.2519 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5213  Z= 0.158
  Angle     :  0.513   5.219   7114  Z= 0.266
  Chirality :  0.043   0.132    760
  Planarity :  0.003   0.022    934
  Dihedral  :  3.574  21.341    712
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.43 %
    Favored  : 81.25 %
  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: -0.35 (0.33), residues: 658
  helix:  1.85 (0.46), residues: 116
  sheet:  0.24 (0.48), residues: 124
  loop : -1.03 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B1014 
 HIS   0.002   0.000   HIS A 910 
 PHE   0.005   0.001   PHE A1164 
 TYR   0.008   0.001   TYR A 993 
 ARG   0.003   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  164)
  hydrogen bonds       : angle       4.06833 (  444)
  SS BOND              : bond        0.00292 (   29)
  SS BOND              : angle       0.76901 (   58)
  covalent geometry    : bond        0.00360 ( 5184)
  covalent geometry    : angle       0.50993 ( 7056)

*********************** 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
  38 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 25
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  931 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7259 (tm-30)
REVERT: A  942 ASP cc_start: 0.8738 (t0) cc_final: 0.8367 (t0)
REVERT: B  931 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7275 (tm-30)
REVERT: B  942 ASP cc_start: 0.8702 (t0) cc_final: 0.8398 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 37
  average time/residue: 0.1466
  time to fit residues: 7.6738
Evaluate side-chains
  29 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 23
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 941 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.070552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.049408 restraints weight = 14874.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 5.06
r_work: 0.2513 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5213  Z= 0.158
  Angle     :  0.522   6.571   7114  Z= 0.265
  Chirality :  0.043   0.126    760
  Planarity :  0.003   0.024    934
  Dihedral  :  3.597  20.871    712
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.07 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.31 (0.34), residues: 658
  helix:  1.91 (0.46), residues: 116
  sheet:  0.20 (0.48), residues: 124
  loop : -0.99 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A1014 
 HIS   0.002   0.000   HIS B1147 
 PHE   0.004   0.001   PHE A 967 
 TYR   0.006   0.001   TYR B1167 
 ARG   0.002   0.000   ARG B1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03728 (  164)
  hydrogen bonds       : angle       3.93723 (  444)
  SS BOND              : bond        0.00277 (   29)
  SS BOND              : angle       0.72760 (   58)
  covalent geometry    : bond        0.00358 ( 5184)
  covalent geometry    : angle       0.51952 ( 7056)

*********************** 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
  41 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 25
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  931 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7386 (tm-30)
REVERT: A  942 ASP cc_start: 0.8802 (t0) cc_final: 0.8557 (t0)
REVERT: B  931 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7335 (tm-30)
REVERT: B  942 ASP cc_start: 0.8703 (t0) cc_final: 0.8391 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 41
  average time/residue: 0.1450
  time to fit residues: 8.5851
Evaluate side-chains
  35 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 23
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.069605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.048600 restraints weight = 14879.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.2697 rms_B_bonded: 5.03
r_work: 0.2510 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8583
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   5213  Z= 0.228
  Angle     :  0.653  11.862   7114  Z= 0.337
  Chirality :  0.046   0.228    760
  Planarity :  0.003   0.023    934
  Dihedral  :  4.032  19.901    712
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.14 %
    Favored  : 79.11 %
  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: -0.31 (0.34), residues: 658
  helix:  1.87 (0.45), residues: 116
  sheet:  0.04 (0.47), residues: 124
  loop : -0.92 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A1090 
 HIS   0.002   0.001   HIS B 910 
 PHE   0.006   0.001   PHE B1217 
 TYR   0.008   0.001   TYR B1167 
 ARG   0.005   0.001   ARG B1190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04273 (  164)
  hydrogen bonds       : angle       4.08391 (  444)
  SS BOND              : bond        0.00553 (   29)
  SS BOND              : angle       2.10153 (   58)
  covalent geometry    : bond        0.00516 ( 5184)
  covalent geometry    : angle       0.62715 ( 7056)

*********************** 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
  44 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 23
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  931 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7761 (tm-30)
REVERT: A  942 ASP cc_start: 0.8838 (t0) cc_final: 0.8571 (t0)
REVERT: B  931 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7382 (tm-30)
REVERT: B  942 ASP cc_start: 0.8761 (t0) cc_final: 0.8456 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 44
  average time/residue: 0.1917
  time to fit residues: 11.1662
Evaluate side-chains
  36 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 22
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  948 THR
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3228 r_free = 0.3228 target = 0.069088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.047796 restraints weight = 14861.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.2664 rms_B_bonded: 5.05
r_work: 0.2473 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   5213  Z= 0.249
  Angle     :  0.606   5.586   7114  Z= 0.316
  Chirality :  0.046   0.166    760
  Planarity :  0.003   0.024    934
  Dihedral  :  4.402  19.460    712
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 17.86 %
    Favored  : 78.93 %
  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: -0.41 (0.33), residues: 658
  helix:  1.77 (0.45), residues: 116
  sheet: -0.05 (0.48), residues: 124
  loop : -0.97 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B1065 
 HIS   0.003   0.001   HIS A 910 
 PHE   0.007   0.001   PHE B1217 
 TYR   0.009   0.001   TYR B 993 
 ARG   0.002   0.000   ARG A1190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04551 (  164)
  hydrogen bonds       : angle       4.27065 (  444)
  SS BOND              : bond        0.00358 (   29)
  SS BOND              : angle       1.15650 (   58)
  covalent geometry    : bond        0.00560 ( 5184)
  covalent geometry    : angle       0.59904 ( 7056)

*********************** 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
  42 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 24
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8830 (t0) cc_final: 0.8511 (t0)
REVERT: B  942 ASP cc_start: 0.8760 (t0) cc_final: 0.8481 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 41
  average time/residue: 0.1724
  time to fit residues: 9.7409
Evaluate side-chains
  37 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 22
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1020 ILE
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  948 THR
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 61 optimal weight:    0.4980
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 = 0.3269 r_free = 0.3269 target = 0.071308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.049991 restraints weight = 14527.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 5.06
r_work: 0.2517 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5213  Z= 0.114
  Angle     :  0.548   5.731   7114  Z= 0.282
  Chirality :  0.044   0.159    760
  Planarity :  0.003   0.027    934
  Dihedral  :  4.017  17.931    712
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.86 %
    Favored  : 79.82 %
  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: -0.31 (0.34), residues: 658
  helix:  1.91 (0.45), residues: 116
  sheet: -0.03 (0.48), residues: 124
  loop : -0.91 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A1014 
 HIS   0.001   0.000   HIS B1147 
 PHE   0.003   0.001   PHE B1028 
 TYR   0.007   0.001   TYR A 993 
 ARG   0.002   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03205 (  164)
  hydrogen bonds       : angle       4.01399 (  444)
  SS BOND              : bond        0.00217 (   29)
  SS BOND              : angle       0.78411 (   58)
  covalent geometry    : bond        0.00271 ( 5184)
  covalent geometry    : angle       0.54542 ( 7056)

*********************** 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
  42 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 29
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8819 (t0) cc_final: 0.8508 (t0)
REVERT: B  942 ASP cc_start: 0.8760 (t0) cc_final: 0.8395 (t0)
  outliers start: 13
  outliers final: 13
  residues processed: 42
  average time/residue: 0.2162
  time to fit residues: 11.7461
Evaluate side-chains
  39 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1228 CYS
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  948 THR
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.071324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.049519 restraints weight = 15056.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.2697 rms_B_bonded: 5.15
r_work: 0.2507 rms_B_bonded: 5.01 restraints_weight: 2.0000
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5213  Z= 0.135
  Angle     :  0.559   6.617   7114  Z= 0.288
  Chirality :  0.044   0.155    760
  Planarity :  0.003   0.027    934
  Dihedral  :  4.014  24.748    712
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.04 %
    Favored  : 79.29 %
  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: -0.31 (0.33), residues: 658
  helix:  1.92 (0.45), residues: 116
  sheet:  0.54 (0.52), residues: 100
  loop : -1.03 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A1090 
 HIS   0.002   0.000   HIS B1147 
 PHE   0.004   0.001   PHE A1217 
 TYR   0.006   0.001   TYR A 993 
 ARG   0.002   0.000   ARG B1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 (  164)
  hydrogen bonds       : angle       3.92367 (  444)
  SS BOND              : bond        0.00243 (   29)
  SS BOND              : angle       0.80567 (   58)
  covalent geometry    : bond        0.00315 ( 5184)
  covalent geometry    : angle       0.55630 ( 7056)

*********************** 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
  41 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 26
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8831 (t0) cc_final: 0.8441 (t0)
REVERT: B  942 ASP cc_start: 0.8762 (t0) cc_final: 0.8407 (t0)
  outliers start: 15
  outliers final: 15
  residues processed: 41
  average time/residue: 0.1952
  time to fit residues: 10.5003
Evaluate side-chains
  40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1228 CYS
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  948 THR
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.071339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.050012 restraints weight = 14525.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 5.01
r_work: 0.2516 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5213  Z= 0.134
  Angle     :  0.575   7.549   7114  Z= 0.297
  Chirality :  0.044   0.155    760
  Planarity :  0.003   0.027    934
  Dihedral  :  3.978  20.781    712
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.21 %
    Favored  : 78.75 %
  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: -0.32 (0.33), residues: 658
  helix:  1.93 (0.45), residues: 116
  sheet:  0.53 (0.52), residues: 100
  loop : -1.04 (0.31), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A1090 
 HIS   0.002   0.000   HIS B1147 
 PHE   0.004   0.001   PHE B1217 
 TYR   0.006   0.001   TYR A 993 
 ARG   0.002   0.000   ARG B1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03396 (  164)
  hydrogen bonds       : angle       3.94217 (  444)
  SS BOND              : bond        0.00236 (   29)
  SS BOND              : angle       0.78420 (   58)
  covalent geometry    : bond        0.00317 ( 5184)
  covalent geometry    : angle       0.57279 ( 7056)

*********************** 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
  43 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 26
  time to evaluate  : 0.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8820 (t0) cc_final: 0.8412 (t0)
REVERT: B  942 ASP cc_start: 0.8765 (t0) cc_final: 0.8402 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 43
  average time/residue: 0.2009
  time to fit residues: 11.1975
Evaluate side-chains
  40 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 25
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1228 CYS
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  948 THR
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3270 r_free = 0.3270 target = 0.071440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.050043 restraints weight = 14576.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 5.02
r_work: 0.2517 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5213  Z= 0.135
  Angle     :  0.585   8.130   7114  Z= 0.302
  Chirality :  0.044   0.154    760
  Planarity :  0.003   0.027    934
  Dihedral  :  4.026  24.002    712
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.21 %
    Favored  : 78.75 %
  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: -0.32 (0.34), residues: 658
  helix:  1.93 (0.45), residues: 116
  sheet: -0.10 (0.48), residues: 124
  loop : -0.90 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A1090 
 HIS   0.002   0.000   HIS B1147 
 PHE   0.006   0.001   PHE A1217 
 TYR   0.006   0.001   TYR A 993 
 ARG   0.004   0.000   ARG A1193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03361 (  164)
  hydrogen bonds       : angle       3.88802 (  444)
  SS BOND              : bond        0.00238 (   29)
  SS BOND              : angle       0.78848 (   58)
  covalent geometry    : bond        0.00319 ( 5184)
  covalent geometry    : angle       0.58325 ( 7056)

********************** 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
  43 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 26
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  942 ASP cc_start: 0.8827 (t0) cc_final: 0.8399 (t0)
REVERT: B  942 ASP cc_start: 0.8763 (t0) cc_final: 0.8395 (t0)
  outliers start: 17
  outliers final: 16
  residues processed: 42
  average time/residue: 0.1898
  time to fit residues: 10.4228
Evaluate side-chains
  41 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 25
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  946 VAL
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  982 VAL
Chi-restraints excluded: chain A residue  998 MET
Chi-restraints excluded: chain A residue 1010 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1181 CYS
Chi-restraints excluded: chain A residue 1200 VAL
Chi-restraints excluded: chain A residue 1228 CYS
Chi-restraints excluded: chain B residue  946 VAL
Chi-restraints excluded: chain B residue  948 THR
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue 1010 LEU
Chi-restraints excluded: chain B residue 1067 LEU
Chi-restraints excluded: chain B residue 1181 CYS
Chi-restraints excluded: chain B residue 1200 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    9.9990
   chunk 3 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 63 optimal weight:    7.9990
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3265 r_free = 0.3265 target = 0.071162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.049656 restraints weight = 14856.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.2699 rms_B_bonded: 5.12
r_work: 0.2505 rms_B_bonded: 5.02 restraints_weight: 2.0000
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5213  Z= 0.150
  Angle     :  0.598   9.278   7114  Z= 0.305
  Chirality :  0.044   0.158    760
  Planarity :  0.003   0.026    934
  Dihedral  :  4.065  24.348    712
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 18.75 %
    Favored  : 78.39 %
  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: -0.32 (0.34), residues: 658
  helix:  1.94 (0.45), residues: 116
  sheet: -0.11 (0.48), residues: 124
  loop : -0.90 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A1090 
 HIS   0.002   0.000   HIS B1147 
 PHE   0.005   0.001   PHE A1217 
 TYR   0.007   0.001   TYR B 993 
 ARG   0.002   0.000   ARG B1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (  164)
  hydrogen bonds       : angle       3.94221 (  444)
  SS BOND              : bond        0.00251 (   29)
  SS BOND              : angle       0.80734 (   58)
  covalent geometry    : bond        0.00351 ( 5184)
  covalent geometry    : angle       0.59633 ( 7056)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2465.34 seconds
wall clock time: 43 minutes 55.15 seconds (2635.15 seconds total)